Methods

Snow depth was determined by averaging ten random samples taken with a meter stick.<br/>

Methods

Phytoplankton samples were obtained from the epilimnion and hypolimnion by
slowly lowering weighted Tygon tubing through the water column to a depth of 7 m, such
that the tubing was filled with a representative water column sample. Based on the inner
diameter of the tubing, 205 mL of water was pumped from the tubing for the epilimnion
sample. Next, 267 mL of water was pumped from the tubing for the hypolimnion sample. Each
sample was collected into a 250 mL amber bottle that contained 2 mL of Lugol’s solution.
Phytoplankton samples were pooled by sampling date and sent to Phycotech Inc. (St. Joseph
MI, USA) for phytoplankton identification, and concentration and biovolume
quantification.<br/>

Methods

Our study lake, South Sparkling Bog (SSB) (46.003°N, 89.705°W), is a bog lake
located in Vilas County in Northern Wisconsin. South Sparkling Bog is a dystrophic,
dimictic lake with a maximum depth of 8 m, a mean depth of 3.6 m, and a surface area of
0.44 ha. South Sparkling Bog is surrounded by a sphagnum bog mat and has no shoreline
development. During the winters of 2019-2020 and 2020-2021, snow was removed from the
surface of South Sparkling Bog following any snow accumulation event. Removal was
conducted via a snowplow attached to the front of an ARGO all-terrain vehicle and a
snowblower. The winter of 2018-2019 served as a reference year, and snow was not removed
from South Sparkling Bog’s surface. While ice cover persisted, plankton samples were
collected at the deep spot for each lake during on a biweekly-to-monthly basis each
winter. On each sampling date, one integrated zooplankton tow was taken at a depth of 0-7
m using a 56 µm mesh Wisconsin net. All zooplankton samples were collected into glass
sample jars, preserved in 90% ethanol, and saved for laboratory analysis. In the lab,
zooplankton samples were filtered through 53 µm mesh and diluted to a known volume, and
three sub-sample replicates were taken using a 1 mL Hensen-Stempel pipette. Sub-sample
replicates were counted to at least 100 individuals, otherwise the entire sample was
quantified. Sub-sample data was then converted to the known diluted volume and finally
converted to total filtered volume (from the integrated tow sample) to estimate density
(individuals L-1). Zooplankton samples were processed using a Leica M8Z dissecting scope
and Leica imaging software. Replicate subsamples were averaged to estimate total abundance
and density, and average lengths (mm) for each sample taxa were calculated from measures
of the first 30 taxa found within a sample date.<br/>

Methods

Nutrients were added to Peter (2013-2015, 2019) and Tuesday (2013-2015)
lakes to cause algal blooms. Details on nutrient additions (start/end dates,
loading rates, N:P ratios) are described in Buelo et al. 2022 (Ecological
Applications, link below), Wilkinson et al. 2018 (Ecological Monographs 88:
188-203), and Pace et al. 2017 (Proceedings of the National Academy of
Sciences USA 114: 352-357). These publications including supplements should
be consulted for details. These lakes have been used for whole-ecosystem
experiments over the past decades; see Carpenter and Pace 2018 (Limnology
and Oceanography Letters 3(6): 419-427) for an overview.<br/>Nutrients were added to Peter (2013-2015, 2019) and Tuesday (2013-2015)
lakes to cause algal blooms. Details on nutrient additions (start/end dates,
loading rates, N:P ratios) are described in Buelo et al. 2022 (Ecological
Applications, link below), Wilkinson et al. 2018 (Ecological Monographs 88:
188-203), and Pace et al. 2017 (Proceedings of the National Academy of
Sciences USA 114: 352-357). These publications including supplements should
be consulted for details. These lakes have been used for whole-ecosystem
experiments over the past decades; see Carpenter and Pace 2018 (Limnology
and Oceanography Letters 3(6): 419-427) for an overview.<br/>Nutrients were added to Peter (2013-2015, 2019) and Tuesday (2013-2015)
lakes to cause algal blooms. Details on nutrient additions (start/end dates,
loading rates, N:P ratios) are described in Buelo et al. 2022 (Ecological
Applications, link below), Wilkinson et al. 2018 (Ecological Monographs 88:
188-203), and Pace et al. 2017 (Proceedings of the National Academy of
Sciences USA 114: 352-357). These publications including supplements should
be consulted for details. These lakes have been used for whole-ecosystem
experiments over the past decades; see Carpenter and Pace 2018 (Limnology
and Oceanography Letters 3(6): 419-427) for an overview.<br/>Nutrients were added to Peter (2013-2015, 2019) and Tuesday (2013-2015)
lakes to cause algal blooms. Details on nutrient additions (start/end dates,
loading rates, N:P ratios) are described in Buelo et al. 2022 (Ecological
Applications, link below), Wilkinson et al. 2018 (Ecological Monographs 88:
188-203), and Pace et al. 2017 (Proceedings of the National Academy of
Sciences USA 114: 352-357). These publications including supplements should
be consulted for details. These lakes have been used for whole-ecosystem
experiments over the past decades; see Carpenter and Pace 2018 (Limnology
and Oceanography Letters 3(6): 419-427) for an overview.<br/>Nutrients were added to Peter (2013-2015, 2019) and Tuesday (2013-2015)
lakes to cause algal blooms. Details on nutrient additions (start/end dates,
loading rates, N:P ratios) are described in Buelo et al. 2022 (Ecological
Applications, link below), Wilkinson et al. 2018 (Ecological Monographs 88:
188-203), and Pace et al. 2017 (Proceedings of the National Academy of
Sciences USA 114: 352-357). These publications including supplements should
be consulted for details. These lakes have been used for whole-ecosystem
experiments over the past decades; see Carpenter and Pace 2018 (Limnology
and Oceanography Letters 3(6): 419-427) for an overview.<br/>Nutrients were added to Peter (2013-2015, 2019) and Tuesday (2013-2015)
lakes to cause algal blooms. Details on nutrient additions (start/end dates,
loading rates, N:P ratios) are described in Buelo et al. 2022 (Ecological
Applications, link below), Wilkinson et al. 2018 (Ecological Monographs 88:
188-203), and Pace et al. 2017 (Proceedings of the National Academy of
Sciences USA 114: 352-357). These publications including supplements should
be consulted for details. These lakes have been used for whole-ecosystem
experiments over the past decades; see Carpenter and Pace 2018 (Limnology
and Oceanography Letters 3(6): 419-427) for an overview.<br/>Nutrients were added to Peter (2013-2015, 2019) and Tuesday (2013-2015)
lakes to cause algal blooms. Details on nutrient additions (start/end dates,
loading rates, N:P ratios) are described in Buelo et al. 2022 (Ecological
Applications, link below), Wilkinson et al. 2018 (Ecological Monographs 88:
188-203), and Pace et al. 2017 (Proceedings of the National Academy of
Sciences USA 114: 352-357). These publications including supplements should
be consulted for details. These lakes have been used for whole-ecosystem
experiments over the past decades; see Carpenter and Pace 2018 (Limnology
and Oceanography Letters 3(6): 419-427) for an overview.<br/>

Methods

Two lakes were studied for two years to test for spatial early warning
statistics (EWS) prior to an experimentally induced algal bloom. In 2018,
both Peter and Paul lakes were unmanipulated and spatial measurements of
each lake were taken weekly from June 6th to August 21st to establish
baseline conditions and EWS values. In 2019, nutrients were added to Peter
Lake while Paul Lake remained an unmanipulated reference lake. Both lakes
were measured three times per week from May 29th to September 4th. More
details on nutrient additions (loading rates, N:P ratios) are provided in
Buelo et al. 2022 (Ecological Applications, link below). <br/>Two lakes were studied for two years to test for spatial early warning
statistics (EWS) prior to an experimentally induced algal bloom. In 2018,
both Peter and Paul lakes were unmanipulated and spatial measurements of
each lake were taken weekly from June 6th to August 21st to establish
baseline conditions and EWS values. In 2019, nutrients were added to Peter
Lake while Paul Lake remained an unmanipulated reference lake. Both lakes
were measured three times per week from May 29th to September 4th. More
details on nutrient additions (loading rates, N:P ratios) are provided in
Buelo et al. 2022 (Ecological Applications, link below). <br/>Two lakes were studied for two years to test for spatial early warning
statistics (EWS) prior to an experimentally induced algal bloom. In 2018,
both Peter and Paul lakes were unmanipulated and spatial measurements of
each lake were taken weekly from June 6th to August 21st to establish
baseline conditions and EWS values. In 2019, nutrients were added to Peter
Lake while Paul Lake remained an unmanipulated reference lake. Both lakes
were measured three times per week from May 29th to September 4th. More
details on nutrient additions (loading rates, N:P ratios) are provided in
Buelo et al. 2022 (Ecological Applications, link below). <br/>Two lakes were studied for two years to test for spatial early warning
statistics (EWS) prior to an experimentally induced algal bloom. In 2018,
both Peter and Paul lakes were unmanipulated and spatial measurements of
each lake were taken weekly from June 6th to August 21st to establish
baseline conditions and EWS values. In 2019, nutrients were added to Peter
Lake while Paul Lake remained an unmanipulated reference lake. Both lakes
were measured three times per week from May 29th to September 4th. More
details on nutrient additions (loading rates, N:P ratios) are provided in
Buelo et al. 2022 (Ecological Applications, link below). <br/>Two lakes were studied for two years to test for spatial early warning
statistics (EWS) prior to an experimentally induced algal bloom. In 2018,
both Peter and Paul lakes were unmanipulated and spatial measurements of
each lake were taken weekly from June 6th to August 21st to establish
baseline conditions and EWS values. In 2019, nutrients were added to Peter
Lake while Paul Lake remained an unmanipulated reference lake. Both lakes
were measured three times per week from May 29th to September 4th. More
details on nutrient additions (loading rates, N:P ratios) are provided in
Buelo et al. 2022 (Ecological Applications, link below). <br/>

Methods

Conducted weekly data sampling (9 boat trips in June-August 2019) using an EXO multi-parameter sonde to collect temperature, conductivity, chlorophyll (ug/L), phycocyanin (ug/L), turbidity, dissolved organic material, ODO, pH, and pressure at 35 locations based on GPS guided stratified random sampling. 35 grid boxes were generated over Lake Mendota using qGIS. Point locations within each grid box were randomized before each sampling effort. At each point, variables were recorded continuously with the EXO sonde for a two-minute period. Continuous data was overaged over the two-minute period for each sample point.

Methods

Protocol available in methods section of: http://msphere.asm.org/content/2/3/e00169-17
Prior to collection, water temperature and dissolved oxygen concentrations are measured using a YSI 550a. The ranges of the epilimnion and hypolimnion are determined based on the location of the thermocline (where temperature/oxygen is changing the fastest). The two layers are collected separately in 1 meter increments using an integrated water column sampler. Water samples are taken back to the lab, shaken thoroughly, and filtered via peristaltic pump through 0.22 micron filters (Pall Supor). Filters are temporarily stored at -20C after collection and then transferred to -80C after transport on dry ice from Trout Lake Station to UW-Madison. Nutrient samples are collected bi-weekly following standard LTER protocols. DNA is extracted from filters using a FASTDNA SpinKit for Soil with minor modifications. (In cases of low yield or specialized sequencing methods, a phenol-chloroform extraction is used instead). The protocol for sequencing and analysis of data varies by year and by sub-project.

Methods

This study used the R packages “GLMr” (https://github.com/GLEON/GLMr) and “glmtools” (https://github.com/USGS-R/glmtools) to interact with GLM-AED from the R statistical environment.

Hourly meteorological data were obtained for 2010-2016 from the North American Land Data Assimilation System (NLDAS) and included air temperature, relative humidity, short wave radiation, long wave radiation, wind speed, rain accumulation, and snow accumulation.

Average daily stream discharge and nitrogen and phosphorus loads were obtained from the United States Geological Survey (USGS) National Water Information System (NWIS) water quality database. All streams included in this study are monitored by the USGS. This study used 2014 nutrient loading data over the simulation time period since 2016 nutrient data were not yet available. Only the Yahara River and Pheasant Branch Creek have data on daily nutrient loads; thus, Pheasant Branch nutrient concentrations were also applied to both Dorn Creek and Sixmile Creek, which contribute near equivalent volume to Lake Mendota. Since GLM-AED requires nutrient concentration rather than load, water column concentrations were back calculated using load and discharge.

Daily OC loads (POC and DOC, individually) were estimated for each individual inflow (n=4) from observed weekly measurements of OC concentration (doi: 10.6073/pasta/86094298f5a9085869518372934bf9d7)
using stream-specific linear models (Lathrop et al. 1998). The linear relationship between known log-scaled OC loads and log-scaled discharge for each individual stream was used to predict the OC load for each day in the model simulation time period. Again, water column OC concentrations were back calculated using the load and discharge.

A manual calibration routine was conducted to optimize the goodness-of-fit of various state variables in GLM-AED, especially those known to influence OC and GHG dynamics. We used visual comparison of predictions and observations, as well as a quantitative approach, to assess goodness-of-fit. We calibrated water balance and water temperature to effectively simulate lake level and stratification. We also calibrated DO, Secchi depth, TN, TP, DOC, and CH4. Finally, we calibrated phytoplankton dynamics according to four phytoplankton functional groups, recognizing that phytoplankton contribute substantially to the OC pool.

Methods

In two consecutive years, we measured lake-wide spatial patterning of cyanobacteria using the FLAMe platform (Crawford et al. 2015). To evaluate early warning indicators of a critical transition, in the first year we induced a cyanobacteria bloom through nutrient addition in an experimental lake while using a nearby unmanipulated lake as a reference ecosystem (Pace et al. 2017). During the second year, both lakes were left unmanipulated. Proposed detection methods for early warning indicators were compared between the manipulated and reference lakes to test for their ability to accurately detect statistical signals before the cyanobacteria bloom developed.
Peter and Paul Lakes are small, oligotrophic lakes (Peter: 2.5 ha, 6 m, 19.6 m and Paul: 1.7 ha, 3.9 m, 15 m, for surface area, mean, and max depth respectively) located in the Northern Highlands Lake District in the Upper Peninsula of Michigan, USA (89°32’ W, 46°13’ N). These lakes have similar physical and chemical properties and are connected via a culvert with Paul Lake being upstream. Both lakes stratify soon after ice-off and remain stratified usually into November (for extensive lake descriptions, see Carpenter and Kitchell, 1993).
In the first year, Peter Lake was fertilized daily starting on 1 June 2015 (DOY 152) with a nutrient addition of 20 mg N m-2 d-1 and 3 mg P m-2 d-1 (molar N:P of 15:1) through the addition of H3PO4 and NH4NO3 until 29 June (day of year, DOY 180). The decision to stop nutrient additions required meeting four predefined criteria based on temporal changes in phycocyanin and chlorophyll concentrations indicative of early warning behavior of a critical transition to a persistent cyanobacteria bloom state. (Pace et al. 2017). Nutrients uniformly mix within 1-2 days after fertilization based on prior studies (Cole and Pace 1998). No nutrient additions were made to Paul Lake. In the second year (2016), neither lake received nutrient additions.
We mapped the surface water characteristics of both experimental lakes to identify changes in the spatial dynamics of cyanobacteria. In 2015, mapping occurred weekly from 4 June to 15 August (11 sample weeks). In 2016, when neither lake was fertilized, the lakes were mapped three times in early to mid-summer. In both years, mapping occurred between the hours of 07:00 to 12:00 (before the daily nutrient addition). We rotated the order that we sampled the lakes to avoid potential biases due to differences in time of day. Each individual lake sampling event was completed in approximately one hour.
The FLAMe platform maps the spatial pattern of water characteristics. A boat-mounted sampling system continuously pumps surface water from the lake to a series of sensors while geo-referencing each measurement (complete description of the FLAMe platform in Crawford et al. 2015). For this study, the FLAMe was mounted on a small flat-bottomed boat propelled by an electric motor and was outfitted with a YSI EXO2™ multi-parameter sonde (YSI, Yellow Springs, OH, USA). We focused for this study on measures of phycocyanin (a pigment unique to cyanobacteria) and temperature. Phycocyanin florescence was measured using the optical EXO™ Total Algae PC Smart Sensor. The Total Algae PC Smart Sensor was calibrated with a rhodamine solution based on the manufacturer’s recommendations. Phycocyanin concentrations are reported as ug/L; however, these concentrations should be considered as relative because we did not calibrate the sensor to actual phycocyanin nor blue-green algae concentrations. Geographic positions were measured using a Garmin echoMAP™ 50s. Sensor- data were collected continuously at 1 Hz and linked via timestamp to create spatially explicit data for each lake. Each sampling produced approximately 3500 measurements in the manipulated lake and 2000 in the reference lake. The measurements were distributed by following a gridded pattern across the entire lake surface to characterize spatial patterns over the extent of the lake.

Methods

This is a compilation of three data sets

North Temperate Lakes LTER: Chemical Limnology of Primary Study Lakes: Nutrients, pH and Carbon 1981 - current
https://lter.limnology.wisc.edu/dataset/north-temperate-lakes-lter-chemical-limnology-primary-study-lakes-nutrients-ph-and-carbon-19

North Temperate Lakes LTER: Physical Limnology of Primary Study Lakes 1981 - current
https://lter.limnology.wisc.edu/dataset/north-temperate-lakes-lter-physical-limnology-primary-study-lakes-1981-current

North Temperate Lakes LTER: Ice Duration - Trout Lake Area 1981 - current
https://lter.limnology.wisc.edu/dataset/north-temperate-lakes-lter-ice-duration-trout-lake-area-1981-current