Methods

One zooplankton sample was collected in June 2015 at the deepest part of each lake, via vertical tow with a Wisconsin net (20cm diameter, 80um mesh). Contents of the net were preserved in the field with cold 95% ethanol. Subsamples of each vertical tow sample were counted for zooplankton species, using enough volume to count at least 300 individuals. A larger volume was then visually scanned to look for presence of additional species not seen in the count volume, until at least 2000 individuals had been seen.

Methods

We collect zooplankton samples at the deepest part of the lake using two different gear types. We take one vertical tow with a Wisconsin Net (80um mesh), and a series of Schindler Patalas (53um mesh) samples spanning the water column. All samples are preserved in cold 95percent EtOH.
After collection we combine subsamples of the individual Schindler Patalas trap samples to create one hypsometrically pooled sample for each lakeordate. The individual depth samples are discarded after pooling except from one August sampling date per year. The Hypsometrically Pooled sample and the Wisconsin Net sample are archived in the UW Zoology museum.
We count zooplankton in one or two subsamples, each representing 1.8L of lake water, of the hypsometrically pooled samples to calculate zooplankton abundance. We count one sample date per month from the open water season, and the February ice cover sample. We identify individuals to genus or species, take length measurements, and count eggs and embryos.
Protocol log: 1981-May1984 -- a 0.5m high, 31L Schindler Patalas trap with 80um mesh net was used. Two Wisconsin Net tows were collected. Preservative was 12percent buffered formalin.
June1984 -- changed to 53um mesh net on Schindler trap.
July1986 -- began using the 2m high, 45L Schindler Patalas trap. Changed WI Net collection to take only one tow.
2001 -- changed zooplankton preservative from 12percent buffered formalin to 95percent EtOH.
The number of sample dates per year counted varies with lake and year, from 5 datesoryear to 17 datesoryear.
1981-1983 -- pooled samples are of several types: Total Pooled (TP) were created using equal volume subsamples of the Schindler samples. Epi, Meta, Hypo pooled used equal volume subsamples from the Schindler samples collected from each of the thermal strata. Strata Pooled used equal volume subsamples from the Epi, Meta, Hypo pooled samples to create an entire lake sample. Hypsometrically Pooled (HP) is our standard, which uses subsample volumes weighted to represent the hypsometry of the lake.

Methods

Fisheries surveys of inland lakes and streams in Wisconsin have been conducted by the Wisconsin Department of Natural Resources (WDNR) professionals and its predecessor the Wisconsin Conservation Department for >70 y. Standard fyke net and boat electrofishing surveys tend to dominate the fisheries surveys and data collected. Most fyke net data on certain species (e.g., Walleye Sander vitreus and Muskellunge Esox masquinongy) originates from annual spring netting surveys following ice-out. These data are used for abundance estimates, mark and recapture surveys for estimating population sizes, and egg-take procedures for the hatcheries. Boat-mounted boom and mini-boom electrofishing surveys became increasingly common in the late 1950s and 1960s. Boat electrofishing surveys have typically been conducted during early summer months (May and June), but some electrofishing survey data are also collected in early spring as part of walleye and muskellunge mark-recapture surveys. Summer fyke netting surveys have been collected more sporadically over time, but were once more commonly used as a panfish survey methodology. Surveys were largely non-standardized. Thus, future users and statistical comparisons utilizing these data should acknowledge the non-standard nature of their collection. More in-depth description of these data can be found in Rypel, A. et al., 2016. Seventy-Year Retrospective on Size-Structure Changes in the Recreational Fisheries of Wisconsin. Fisheries, 41, pp.230-243. Available at: http://afs.tandfonline.com/doi/abs/10.1080/03632415.2016.1160894

Methods

Fisheries surveys of inland lakes and streams in Wisconsin have been conducted by the Wisconsin Department of Natural Resources (WDNR) professionals and its predecessor the Wisconsin Conservation Department for >70 y. Standard fyke net and boat electrofishing surveys tend to dominate the fisheries surveys and data collected. Most fyke net data on certain species (e.g., Walleye Sander vitreus and Muskellunge Esox masquinongy) originates from annual spring netting surveys following ice-out. These data are used for abundance estimates, mark and recapture surveys for estimating population sizes, and egg-take procedures for the hatcheries. Boat-mounted boom and mini-boom electrofishing surveys became increasingly common in the late 1950s and 1960s. Boat electrofishing surveys have typically been conducted during early summer months (May and June), but some electrofishing survey data are also collected in early spring as part of walleye and muskellunge mark-recapture surveys. Summer fyke netting surveys have been collected more sporadically over time, but were once more commonly used as a panfish survey methodology. Surveys were largely non-standardized. Thus, future users and statistical comparisons utilizing these data should acknowledge the non-standard nature of their collection. More in-depth description of these data can be found in Rypel, A. et al., 2016. Seventy-Year Retrospective on Size-Structure Changes in the Recreational Fisheries of Wisconsin. Fisheries, 41, pp.230-243. Available at: http://afs.tandfonline.com/doi/abs/10.1080/03632415.2016.1160894

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

the protocol employed here is based on:
Hauxwell, J., S. Knight, K. Wagner, A. Mikulyuk, M. Nault, M. Porzky and S. Chase . 2010. Recommended baseline monitoring of aquat ic plants in Wisconsin : sampling design, field and laboratory procedures, data entry and analys is, and applica tions. Wisconsin Department of Natural Resources Bureau of Science Services, PUB-SS-1068 2010. Madison, Wisconsin, USA.

Methods

The BCC of three small northern Wisconsin lakes, CB (polymictic, maximum depth 2.5 m), TB (dimictic, maximum depth 7 m) and MA (meromictic, maximum depth 21.5 m), were sampled weekly during the open-water period of 2005 (late May to early November). These lakes were chosen because of their shared dystrophy, acidity, similar surface area (range 0.6–1.2 ha), comparable physicalorchemical characteristics, proximity to one another and range of annual of mixing frequencies. Samples were collected over the deepest point of each lake. All lakes were sampled on the same day each week.Temperature and DO measurements were observed for every sample date using YSI model 58 dissolved oxygen meter (Yellow Springs, OH) calibrated at each sample date as per manufacturer s instruction. Trout Bog and MA profiles were observed at every metre and CB profiles were observed at every half metre. Integrated water column samples were collected for each thermal layer. Thermal layer boundaries were determined based on temperature profiles. The top of the hypolimnion was determined to be where the temperature decreased by 1.5–2.0degreeC over 0.5 m or less. In polymictic CB, the epilimnion was consistently sampled at 0.0–1.0 m, and the hypolimnion at 1.0–2.0 m; these depths were based on thermal profiles of CB s weak stratification (rate of change of 0.5degreeC m−1 or greater), as observed in instrumented buoy temperature profiles available from the Global Lakes Ecological Observatory Network database (GLEON, http:ororwww.gleon.org). According to buoy data temperature profiles, CB mixed a minimum of nine times over the sampling season in 2005.Bacterial cells were immediately recovered from 100 to 250 ml of lake sample water by filtration onto a 0.2 μm polyestersulfone filter (Pall, New York, NY), and stored at −80degreeC until further processing.Mean difference in DO and temperature for each layer was calculated by averaging the profile observations included in the layer of interest for each sample date, and then subtracting the average of the hypolimnion profile from the epilimnion. These differences were then averaged over the entire sampling period when a global mean was desired.Additional physical and chemical data for TB and CB were provided by the North Temperate Lakes Long-term Ecological Research (NTL-LTER) and the Center for Limnology at University of Wisconsin-Madison.

Methods

Experimental designThe experiment was conducted from 16 to 26 June 2008. In the first treatment, oxygen was added to the hypolimnion. In the second, nutrients were added to the epilimnion. The third treatment simulated a mixing event (overturn). There also was a control enclosure with no treatment and sampling of the ambient lake water. Throughout this manuscript, we refer to these as Oxygen, Nutrient, Mix, Control and Ambient.Twelve limnocorrals were constructed as enclosures for the experiment. Each limnocorral was cylindrical and extended vertically from the surface of the lake to the sediment (approximately 4 m). The total volume was approximately 5050 l. Details of limnocorral construction are provided in online Supporting Information.The limnocorrals were deployed on 15 June 2008 to allow the sediment and water column to stabilize before treatment on 16 June 2008. The limnocorrals were deployed in a random spatial arrangement throughout the lake, at a maximum depth of 3.25 to 3.5 m. Replicates from each treatment were instrumented with a chain of HOBO temperature sensors (Onset), and one replicate from each had a self-logging DO sonde (Yellow Springs Incorporated) in the hypolimnion (3 m depth). More thermistors were deployed in the Oxygen and Mix treatments because thermal stratification was important for evaluating success of these treatments.For the Mix treatment, a 60 cm flat disk was raised and lowered between 3.5 m depth and the lake surface. Holes were drilled through the disk surface to increase turbulence (Sanford, 1997; Regel et al., 2004). A brick was tied underneath the disk to maintain stability. We manually oscillated the disk every 10 min for 1 h and then, after a 1 h break, continued for an additional hour. Temperature and DO profiles were monitored within the limnocorral with a hand-held probe to track mixing progress.The goal of the Oxygen treatment was to aerate the hypolimnion water without allowing it to mix with the epilimnion. This treatment was achieved by pumping hypolimnion water from the bottom of the limnocorral into an external cooler where the water was aerated with bubble diffusers, and then returned to the bottom of the limnocorral (Fig. S1). Valves on a compressed air cylinder were used to control the delivery of air to the coolers. One cooler was maintained for each replicate limnocorral. Thermally insulated tubing was used to transport water. A thermistor was deployed in each cooler to ensure ambient hypolimnion temperature was maintained. The water was removed and returned using two linear diffusers that were 0.6 m in length, spanning a depth range of approximately 2.5–3.1 m within the hypolimnion. The diffusers faced inward with 0.5 m fixed distance between them, retained by a plastic divider. This treatment was applied continuously over 3 h, until DO concentrations increased.The Nutrient treatment was achieved by adding ammonium chloride (NH4Cl) and potassium phosphate monobasic (KH2PO4) as N and P sources. These compounds were chosen because they are commonly bioavailable sources of nutrients. P was added to the epilimnion to achieve a final concentration of 3 micro g P l−1, which was approximately the average concentration expected in the mixed water column. This value was based on nutrient analyses from integrated water collected on 9 June 2008 in North Sparkling Bog, a week prior to experiment start. Similarly, N was added to achieve a final concentration of 70 µg N l−1. The limnocorral s epilimnion volume (0–2 m integrated depth) was calculated to be 2520 l, and we used the molar mass to determine the amount of each nutrient added to the epilimnion to achieve the expected mixed concentration. Dry chemicals were dissolved into to 500 ml of surface water from each limnocorral, and then added into each separately. Rationale for directly manipulating only one layer in the Oxygen and Nutrient treatments is given in the online Supporting Information.The Control limnocorrals were left undisturbed. To prevent mixing during equipment removal, all tubing was left inside the limnocorrals until the experiment ended.

Methods

Sampling Frequency: bi-weekly during ice-off from 2000 to 2005Total number of observations: 82Number of sites: 1 site over the deep hole of the lake (Lake Mendota, 89degree 24 W long, 43degree 06 N lat)Sampling techniques: integrated 0-12 mNomenclature:Lake name is ME. Sample IDs are ME-date with date = MM-DD-YY.DNA extraction protocol: FastPrep DNA extraction kitBinning protocol: Manual in GeneScanorGenotyperCapillary Instrument (from Biotech Center): ABI 3700PCR DNA standardization protocol: By volume of lake water filteredPCR thermocycler protocol:RISA30x protocol: 2 min 94C, [35s. Denature 94C, 45 s. Annealing 55C, 2 min Extension 72C (rep 30x)], 2 min extension 72C.Analyses performed other than ARISA:Additional comments:Raw ABI files are in two batchesBatch 1: Duplicate samples from 2000-2004 with nomenclature basically the same as the sample IDs plus the replicate number, such as ME 2-28-02 rep1. Note that the month is not 2-digit unless it has two digits.Batch 2: Duplicate samples from 2000-2005 with nomenclature as ME-date where date is DD-month-YY and the replicate number, such as ME 27Apr00 rep1.NOTE: We are not sure which samples were used for the final analysis. They must have been a blend of the two batches. Contact Ashley Shade (ashley17061atgmail.com) for clarification if needed.

Methods

BOOM SHOCKING1987:A standard WDNR electrofishing boat was used on Lake Mendota set at 300 volts and 2.5 amps (mean) DC, with a 20 % duty cycle and 60 pulses per second. On all sampling dates two people netted fish, the total electrofishing crew was three people. Shocking was divided into stations. For each station, the actual starting and ending time was recorded. Starting and ending points of each station were plotted on a nap. A 7.5 minute topographic map (published 1983) and a cartometer was used to develop a standardized shoreline mileage numbering scheme. Starting at the Yahara River outlet at Tenney Park and measuring counterclockwise, the shoreline was numbered according to the number of miles from the outlet. The length of shoreline shocked for each station was determined using the same maps. The objectives of the fall 1987 electrofishing was: to gather CPE data for comparison with previous surveys of the lake; develop a database for relating fall electroshocker CPE to predator density; collect fall predator diet data; make mark-recapture population estimates of YOY predators; and determine year-class-strength of some nonpredators (yellow perch, yellow bass, and white bass).1993: Electrofishing was used to continue marking largemouth and smallmouth bass (because of low CPE in fyke nets), to recapture fish marked in fyke netting, and to mark and recapture walleyes ( less than 11.0 in.) on Lake Mendota. Four person crews electrofished after sunset from May 05 to June 03, 1993. A standard WDNR electrofishing boat was used, set at about 300 volts and 15.0 amps (mean) DC, with a 20 % duty cycle at 60 pulses per second. On all sampling dates two people netted fish; thus, CPE data are given as catch per two netter hour or mile. Shocking was divided into stations. For each station the actual starting and ending time and the generator s meter times was recorded. Starting and ending points of each station were plotted on a map. 7.5 minute topographic maps (published in 1983) were used in addition to a cartometer to develop a standardized shoreline mileage numbering scheme. Starting at the Yahara River outlet at Tenney Park and measuring counterclockwise the shoreline was numbered according to the number of miles from the outlet. The length of shoreline shocked for each station was determined using these maps. The 4 person electroshocker crews were used again from September 20 to October 19. Fall shocking had several objectives: to gather CPE data for comparison with previous surveys of the lake; develop a database for relating fall electroshocker CPE to piscivore density; and make mark recapture population estimates of young of year (YOY) piscivores.1997:5/13/1997-5/20/1997: Electrofishing was completed at night on lakes: Mendota, Monona, and Waubesa. A standard WDNR electrofishing boat was used, set from 320-420 volts and 16-22 amps DC, with a 20 % duty cycle at 50 pulses per second. Two netters were used for each shocking event. At a particular station, starting and ending times where shocking took place were recorded. The location of the designated shocking stations is unknown.9/23/1997-10/14/1997: Electrofishing was completed at night on Mendota, Monona, Waubesa, and Wingra. A standard WDNR electrofishing boat was used, set from 315-400 volts and 16-24 amps DC, with a 20% duty cycle at 60 pulses per second. Two netters were used for each shocking event. Starting and ending time at each shocking station was listed. The location of the designated shocking stations is unknown.1998:Electrofishing was completed at night on Mendota, Monona, Wingra, and Waubesa from 5/12/1998- 10/28/1998. A standard WDNR electrofishing boat was used, set from 240-410 volts and 15-22 amps DC, with a 20% duty cycle at 50-100 pulses per second. Two netters were used for each shocking event. Starting and ending time at each shocking station was listed. The location of the designated shocking stations is unknown. FYKE NETTING1987:Fyke nets were fished daily from March 17 to April 24, 1987 on Lake Mendota. The nets were constructed of 1.25 inch (stretch) mesh with a lead length of 50 ft. (a few 25 ft. leads were used). The hoop diameter was 3 ft. and the frame measured 3 ft. by 6 ft. Total length of the net was 28 ft. plus the lead length. Nets were set in 48 unknown locations. Initially, effort was concentrated around traditional northern pike spawning sites (Cherokee Marsh, Sixmile Creek, Pheasant Branch Creek, and University Bay). As northern pike catch-per-effort (CPE) declined some nets were moved onto rocky shorelines of the lake to capture walleyes. All adult predators (northern pike, hybrid muskie, largemouth and smallmouth bass, walleye, gar, bowfin, and channel catfish) captured were tagged and scale sampled. Measurements on non-predator species captured in fyke nets were made one day per week. This sampling was used to index size structure and abundance, and to collect age and growth data. In each net, total length and weight of 20 fish of each species caught was measured, and the remaining caught were counted.1993:Same methods as 1987, except fyke nets were fished from 4/8/1993-4/29/1993 on Lake Mendota. The 1993 fyke net data also specifies the &ldquo;mile&rdquo; at which the fyke net was set. This is defined as the number of miles from the outlet of the Yahara River at Tenney Park, moving counterclockwise around the lake. In addition, abundance and lengths of non-gamefish species captured in fyke nets were recorded one day per week. Six nets were randomly selected to sample for non-gamefish data. This sampling was used to index size structure and abundance, and to collect age and growth data. In each randomly selected net, total length and weight was measured for 20 fish of each species, and the remaining caught were counted.1998:There is no formal documentation for the exact methods used for fyke netting from 3/3/1998-8/12/1998 on Lake Mendota. However, given that the data is similar to data collected in 1987 and 1993 it is speculated that the same methods were used.MINI-FYKE NETTING1989:There is no formal documentation for the exact methods used for mini-fyke netting on Lake Mendota and Lake Monona from 7/26/1989-8/25/1989. However, given that the data is similar to data collected from 1990-1993 it is speculated that the same methods were used. In the sampling year of 1989, mini-fyke nets were placed at 22 different unknown stations.1990-1993: Mini-fyke nets were fished on Lake Mendota and Lake Monona during July-September at 20, 29, 13, and 15 sites per month during 1990, 1991, 1992, and 1993, respectively to estimate year-class strength, relative abundance, and size structure of fishes in the littoral zone. Nets were constructed with 3/16 in. mesh, 2 ft. diameter hoops, 2 ft. x 3 ft. frame, and a 25 ft. lead. Sites were comparable to seine sites used in previous surveys. Sites included a variety of substrate types and macrophyte densities. To exclude turtles and large piscivores from minifyke nets, some nets were constructed with approximately 2 in. by 2 in. mesh at the entrance to the net. Thus, mini-fyke net data are most accurate for YOY fishes, and should not be used to make inferences about fishes larger than the exclusion mesh size. 1997:There is no formal documentation for the mini-fyke methods which were used on Lake Waubesa and Lake Wingra from 9/16/1997-9/18/1997. However, given that the data is similar to data collected in 1989, and 1990-1993, it is speculated that the methods used during 1997 are the same. SEINE NETTING1989, 1993: Monthly shoreline seining surveys were conducted on Lake Mendota and Lake Monona during June through September to estimate year class-strength, relative abundance, and size structure of the littoral zone fish community. Twenty sites were identified based on previous studies. Sites included a variety of substrate types and macrophyte densities. Seine hauls were made with a 25ft bag seine with 1/8 inch mesh pulled perpendicular to shore starting from a depth of 1 m. Twenty fish of each species were measured from each haul and any additional fish were counted. Gill Netting (1993)Experimental gill nets were fished in weekly periods during June through August, 1993. Gill nets were used to capture piscivores for population estimates of fish marked in fyke nets. All nets were constructed of five 2.5-4.5 in. mesh panels, and were 125 ft. long. Nets set in water shallower than 10 ft. were 3ft. high or less; all others were 6ft. high or less. Sampling locations were selected randomly from up to three strata: 1) offshore reef sets, 2) inshore sets, 6.0-9.9 ft. deep, and 3) mid-depth sets, 10-29.9 ft. deep. The exact location at which the gill nets were set on the lake is unknown because the latitude and longitude values which were recorded by the WDNR are invalid. Temperature and dissolved oxygen profiles were used to monitor the development of the thermocline and guide net placement during July and August. After the thermocline was established nets were set out to the 30 ft. contour or to the maximum depth with dissolved oxygen greater than 2 ppm. Walleye Age: Scale and Spine Analysis (1987) Scales were taken from walleye that were shocked during the fall of 1987 electrofishing events on Lake Mendota. Scales were taken from 10 fish per one-inch length increment. The scales were removed from behind the left pectoral fin, and from the nape on the left side on esocids. In addition, the second dorsal spine was removed from 10 walleyes per sex and inch increment (to age and compare with scale ages for fish over 20 inches). CREEL SURVEYS1989:Fishing pressure, catch rates, harvest, and exploitation rates were estimated from a randomized, access-point creel survey. The schedule was stratified into weekday and weekend/holiday day types. Shifts were selected randomly and were either 07:00-15:00 h or 15:00-23:00 h. In addition, two 23:00-03:00 h shifts and two 03:00-07:00 h shifts were sampled per month to estimate the same parameters during night time hours. During the ice fishing season (January-February) 22 access points around Lake Mendota and upstream to the Highway 113 bridge were sampled. The clerk counted the number of anglers starting and completing trips during the scheduled stop at each access point. During openwater (March-December) 13 access points were sampled; 10 were boat ramps and 3 were popular shore fishing sites<strong>. </strong>At each of these sites, an instantaneous count of shore anglers was made upon arrival at the site, continuous counts of anglers starting and completing trips at public and private access points were made. Boat occupants and ice fishing anglers were only interviewed if they were completing a trip. Both complete and incomplete interviews were made of shore anglers. Number caught and number kept of each species, and percent of time seeking a particular species were recorded. All predators possessed by anglers were measured, weighed, and inspected for finclips and tags. We measured a random sample of at least 20 fish of each non-predator species per day.1990-1993: Same as 1989, except 23 access points were used during the ice fishing season. In addition, 13 access points were sampled during the openwater (May-December) season; 9 sites were boat ramps and 4 sites were popular shore fishing sites. 1994-1999: No formal documentation exists, but given the similarity in the data and consistency through the years; it is speculated tha tthe methods are the same.