Methods

Data were collected from two lakes, Sparkling Lake (46.008, -89.701) and Peter Lake (46.253, -89.504), both located in the northern highlands Lake District of Wisconsin and the Upper Peninsula of Michigan over a 10 day period on each lake in July and August of 2007. Refer to Van de Bogert et al. 2011 for limnological characteristics of the study lakes.Measurements of dissolved oxygen and temperature were made every 10 minutes using multiple sondes dispersed horizontally throughout the mixed-layer in the two lakes (n=35 sondes for Sparkling Lake and n=27 sondes for Peter Lake). Dissolved oxygen measurements were corrected for drift.Conductivity, temperature compensated specific conductivity, pH, and oxidation reduction potential were also measured by a subset of sensors in each lake. Of the 35 sondes in Sparkling Lake, 31 were from YSI Incorporated: 15 of model 600XLM, 14 of model 6920, and 2 of model 6600). The remaining sondes placed in Sparkling Lake were 4 D-Opto sensors, Zebra-Tech, LTD. In Peter Lake, 14 YSI model 6920 and 13 YSI model 600XLM sondes were used.Sampling locations were stratified randomly so that a variety of water depths were represented, however, a higher density of sensors were placed in the littoral rather than pelagic zone. See Van de Bogert et al. 2012 for the thermal (stratification) profile of Sparkling Lake and Peter Lake during the period of observation, and for details on how locations were classified as littoral or pelagic. In Sparkling Lake, 11 sensors were placed within the shallowest zone, 12 in the off-shore littoral, and 6 in each of the remaining two zones, for a total of 23 littoral and 12 pelagic sensors. Similarly, 15 sensors were placed in the two littoral zones, and 12 sensors in the pelagic zone.Sensors were randomly assigned locations within each of the zones using rasterized bathymetric maps of the lakes and a random number generator in Matlab. Within each lake, one pelagic sensor was placed at the deep hole which is used for routine-long term sampling.Note that in Sparkling Lake this corresponds to the location of the long-term monitoring buoy. After locations were determined, sensors were randomly assigned to each location with the exception of the four D-Opto sensor is Sparkling Lake, which are a part of larger monitoring buoys used in the NTL-LTER program. One of these was located near the deep hole of the lake while the other three were assigned to random locations along the north shore, south shore and pelagic regions of the lake. Documentation: Van de Bogert, M.C., Bade, D.L., Carpenter, S.R., Cole, J.J., Pace, M.L., Hanson, P.C., Langman, O.C., 2012. Spatial heterogeneity strongly affects estimates of ecosystem metabolism in two north temperate lakes. Limnology and Oceanography 57, 1689-1700.

Methods

I. Stream chemistry sample collection methods: core-sediment core was taken from the benthic zone of the streamgeopump-geopump used to pump stream water into collection bottlegrab-collection bottle filled with stream water by hand and filtered in the fieldgrabfilter- stream water collected by hand and filtered in field. Unfiltered and filtered samples placed in separate collection bottles.isco- sample collected by use of an ISCO automated samplerpoint- sampled collected by method outlined in patent US8337121sedimentgrab- sediment sample taken in field by hand and placed in collection bottlesyringe- sample collected from stream by syringe and placed in collection bottlesyringe_filter- sample collected from stream by syringe filter. Unfiltered and filtered samples placed in separate collection bottles. II. Stream chemistry analytical methods: All water samples were kept on ice and in the dark following collection, then were either acidified (TN/TP, TDN/TDP) or frozen until analysis (all other analytes).no32_2- This is NO_3-N which is operationally defined as nitrate nitrogen + nitrite nitrogen. Determined by flow injection analysis on Astoria Pacific Instruments Autoanalyzer (APIA).nh4_n, tn1, tp1, tdn, tdp- All analytes measured by flow injection analysis on Astoria Pacific Instruments Autoanalyzer (APIA).srp- measured colorometrically using the molybdate blue method [APHA 1995] and a Beckman spectrophotometer.doc- measured using a Shimadzu carbon analyzer.doc_qual- the goal in doing this analysis is to determine the source of dissolved organic carbon (doc) measured in a particular riverine ecosystem. This was achieved by UV absorbance which provides an estimate of the aromaticity of the doc in a sample, and by extension, the potential source of the doc.cl, no2, no3, br, and so4- all measured by ion chromatography. See http://www.nemi.gov; method number 4110C. Detection limits for method number 4110C: cl-20&micro;g/l, no2-15&micro;g/l, no3-17&micro;g/l, br-75&micro;g/l, and so4-75&micro;g/l.ysi_cond, do, ph_field, wtemp- all measured by use of a standard YSI meter.tss- measured by standard methods. A thoroughly mixed sample is filtered and dried at 103-105 degreesCelcius. The obtained residue represents the amount of solids suspended in the sample solution. See http://www.nemi.giv; method number D5907.tot_om- measured by standard methods. The residue obtained from the tss procedure is ignited at 550 degreesCelcius and weighed, the difference in weight representing total volatile solids. Total volatile solids represents the portion of the residue that is composed of organic molecules. See http://www.nemi.gov; method number 160.4.turbid- measured by use of a nephelometer. III. Big Spring Sediment Coring Methods A. Field Methods- collecting sediment coresSediment core samples taken with WDNR piston core samplerB. Sediment Analysis- HydrometerDocumentation: Robertson, G.P., Coleman, D.C., Bledsoe, C.S. and Sollins, P., 1999. Standard Soil Methods for Long-Term Ecological Research. Oxford University Press, New York, 462 pp.Hydrometer Analysis- procedure used to determine percent clay:<p style="margin-left:.25in;">1. Dry the sample in a pre-weighed aluminum pan for at least 24 hr at 105 C. Make sure sample is completely dry before weighing.<p style="margin-left:.25in;">2. Weigh the dried sample, then ash for at least 8 hr at 550 C. Make sure to break up any large clumps before ashing.<p style="margin-left:.25in;">3. Weigh the ashed sample, then crush any aggregates with a pestal. Mix sample thoroughly.<p style="margin-left:.25in;">4. Transfer 40g, plus or minus one gram, of the sample into a 500mL wide mouth bottle<p style="margin-left:.25in;">5. Add 10g of sodium hexametaphosphate to the bottle.<p style="margin-left:.25in;">6. Add approx 200mL of deionized water to bottle. Shake vigorously with hand.<p style="margin-left:.25in;">7. Stir samples on shaker table for at least 8 hr at speed 40. Putting them in a box and fastening with bungee cords works best.<p style="margin-left:.25in;">8. Transfer sample to 1L cylinder, making sure to get all of sample out of bottle. Fill cylinder with deionized water up to the 1L mark.<p style="margin-left:.25in;">9. Prepare a blank cylinder by adding 10g of sodium hexametaphosphate and filling to 1L.<p style="margin-left:.25in;">10. Allow all cylinders to equilibrate to room temperature ( approx 30 min).<p style="margin-left:.25in;">11. Starting with the blank cylinder, put stopper into cylinder and shake end-over-end for approx 5 min. Rinse stopper. Repeat this step for all cylinders, rinsing stopper between cylinders.<p style="margin-left:.25in;">12. Record the time that you stopped shaking each cylinder.<p style="margin-left:.25in;">13. At 1.5 hr from time of shaking, record temperature and hydrometer level of the blank cylinder. Then record the 1.5 hr hydrometer level for each successive cylinder.<p style="margin-left:.25in;">14. At 24 hr from time of shaking, record temperature and hydrometer level of the blank cylinder. Then record the 24 hr hydrometer level for each successive cylinder. Sieve Analysis- procedure used to determine quantity of sand and silt<p style="margin-left:.25in;">1. After hydrometer analysis, pour the entire sample into the .063mm sieve. Rinse the sample thoroughly until all the clay is out. Try to break up any clay clumps you see.<p style="margin-left:.25in;">2. Transfer the sample to a pre-weighed and labeled aluminum pan. You will probably need to backwash the sieve to get the entire sample out. You can use a syringe to pull water from the pan if it gets too full. Dry the sample for 48 hours at 50-60C.<p style="margin-left:.25in;">3. Before transferring the dried sample to the sieves, make sure you pre-weigh the sieves and put their weight on the data sheet. You will need to do this before every sample as you might not get all the sample out of the sieves from the previous sample. Stack the sieves in the following order, top to bottom : 4mm, 2mm, 1mm, 0.5mm, 0.25mm, 0.125mm, 0.063mm, and pan. Pour the sample into the top sieve. Place the lid on, located on sieve shaker, and put the stack of sieves into the sieve shaker. Fasten the tie downs. Set shaker for 3 minutes. <p style="margin-left:.25in;">4. Remove stack of sieves from shaker. It&rsquo;s ok to leave the pan behind temporarily as it might be tight. Weigh each sieve and record the weight in the data sheet. If you see any clay clumps, break them up with your fingers and re-shake the stack a little, using hands is okay.<p style="margin-left:.25in;">5. Dump the sample out in the trash and clean the sieve with the brush. At the end of the day it might be necessary to backwash the sieves with water and dry overnight in the oven. <p style="margin-left:.25in;"> Calculations:1. percent clay was determined by the hydrometer analysis- P1.5, P24, X1.5, X24, and m are the variables that were calculated to determine percent clay by the hydrometer analysis.P1.5= ((sample hydrometer reading at 1.5 hours- blank hydrometer reading at 1.5 hours)/ (sample weight)) multiplied by 100.P24= ((sample hydrometer reading at 24 hours- blank hydrometer reading at 24 hours)/ (sample weight)) multiplied by 100X1.5= 1000*(.00019*(-.164* (sample hydrometer reading at 1.5 hours)+16.3)² *8100X24=1000*(.00019*(-.164* (sample hydrometer reading at 24 hours)+16.3)² *8100m= (P1.5-P24)/(ln(X1.5/X24))percent clay = m * ln(2/X24)) + P24clay (grams) = total weight * ( percent clay/ 100)2. percent Sand and percent Silt were determined based on the results of the sieve analysis which determined the grams of sand and silt.percent sand= total weight * (percent sand/ 100)percent silt= total weight * (percent silt/ 100)3. Othersorganic matter (grams) was calculated in this analysis as dry weight (grams) &ndash; ashed weight (grams)percwnt organic matter was calculated as ((organic matter (grams))/(total dry weight (grams)) multiplied by 100 C. Sediment Chemical Analysis1. SRP/ NaOH-PChemical analysis was done according to the protocol outlined in Pionke and Kunishi (1992). Each sample was first centrifuged and separated into aqueous and sediment fractions. The sediment fraction was then dried. The aqueous fraction was analyzed for soluble reactive phosphorus (srp) by automated colorimetry Nemi Method Number 365.4; see http://www.nemi.gov. NaOH P was then determined by NaOH extractions as described in Pionke and Kunishi (1992). Documentation: Pionke HB, Kunishi HM (1992) Phosphorus status and content of suspended sediment in a Pennsylvania watershed. Soil Sci 153:452&ndash;462.2. NH4 / KCl-NH4 The exact procedure that was used to analyze samples for ammonium is unknown. However, it is known that a KCl extraction was used. The KCl-NH4 was calculated as the concentration of ammonium in milliGramsPerLiter divided by the sediment weight in grams. 3. NO3 / KCl-NO3The exact procedure that was used to analyze samples for nitrate is also unknown. Again, it is known that a KCL extraction was used. The KCl-NO3 was calculated as the concentration of nitrate in milliGramsPerLiter divided by the sediment weight in grams.Note: The same sediment sample was used to measure ammonium and nitrate IV. Big Spring Creek Longitudinal Profile A standard longitudinal stream profile was conducted at Big Spring Creek, WI (wbic=176400) on unknown date(s). It is speculated that the profile was done during the summer of 2005, during which the rest of the data for Big Spring Creek was collected. Measurements for the profile began at the Big Spring Dam site (43.67035,-89.64225), a dam which was subsequently removed. The first (x_dist, y_dist) of (2.296, 5.57) corresponds to the location where the stream crosses Golden Court Road, whereas the second coordinate pair of (-2.615, -36.303) corresponds to the point below the previous Big Spring Creek Dam site. The third (x_dist, y_dist) of (-9.472, 7.681) corresponds to the top of the dam gates and is assigned a distance=0 as it is the starting point.

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.

Methods

Hanson PC, Carpenter S, Cardille JA, Coe MT, Winslow LA. 2007. Small lakes dominate a random sample of regional lake characteristics. Freshwater Biology. 52:814-22Lakes were selected from unique Water Body Identification Codes (WBICs). Linear features and water bodies identified as impoundments or stream openings were identified from maps digitised by the Departments of Natural Resources of Michigan and Wisconsin (1 : 24 000 USGS 7.5&rsquo; topographic quadrangles) and were excluded. More than 7500 lakes ranging in size from about 0.01 to over 2800 ha remained in the data set. We used a stratified random survey, an approach consistent with the Environmental Monitoring and Assessment Program (EMAP) guidelines (Larsen et al., 1994) of the U.S. Environmental Protection Agency, to select and sample 300 lakes from the data set as follows. All lakes were ordered by area and divided into 20 bins of equal population. From each bin, 15 lakes were chosen at random. Because of logistical issues in travelling to many lakes scattered over a wide geographical region, we clustered lakes into 31 geographically small regions of about 150 km2 each. The order of regions sampled was randomised to reduce correlation of geographic region with time. For any one sampling date we visited only one region, although not all lakes in a region could be visited on a single trip. After all 31 regions were visited, the regions were again selected at random, and lakes previously not visited were sampled. There were 45 sampling days spread between May 20 and August 19. Some lakes that were chosen for sampling could not be visited. Difficulty portaging the sampling gear to a lake or failure to gain access to a lake through private property were reasons for abandoning a sampling effort.Lakes were sampled at their approximate geographic centre. Lake depth and water clarity were measured with a Secchi disk. Our measurement of lake depth was neither a measurement of the maximum nor the mean depth. Because the measurement was made in the middle of the lake and most lakes in the region tend to be bowl shaped, our measurement was probably between mean and maximum depth. Dissolved oxygen (DO) and thermal profiles were obtained from a YSI Model 58 (YSI, Inc., Yellow Springs, OH, U.S.A.) metre (DO air calibrated; temperature calibrated in the laboratory), and the approximate middle of the epilimnion was estimated from the profile. Thermal stratification was calculated from the thermal profile according to the methods listed on the Internet at the North Temperate Lakes Long Term Ecological Research (NTL-LTER) program Web site (http://lter.limnology.wisc.edu). Water samples for later analyses (Table 1, chemical variables) were obtained from the middle of the epilimnion, using a peristaltic pump. For samples that required filtration [dissolved inorganic carbon (DIC), DOC, cations and anions], a 0.45 μm filter was attached in-line. All samples were refrigerated upon returning to the vehicle, and samples for total nitrogen (TN) and total phosphorus (TP) were preserved by acidification. Acid neutralizing capacity (ANC) and pH were determined the day of sampling by Gran alkalinity titration (for ANC) and measurement by pH probe (Accumet 950; Fisher Scientific, Hanover Park, IL U.S.A.). pH was not air equilibrated. DIC and DOC were measured with a carbon analyzer (TOC-V; Shimadzu Scientific Instruments, Columbia, MD, U.S.A.). TN and TP were measured with a segmented flow auto-analyzer (Astoria-Pacific, Inc., Clackamas, OR, U.S.A.). Anions were measured using an ion chromatograph (DX500; Dionex Corporation, Sunnyvale, CA, U.S.A.), and cations using mass spectrometry (ICP-MS; PerkinElmer Life and Analytical Sciences, Shelton, CT, U.S.A.). Details of chemical analyses are available on the Internet at the NTL-LTER Web site listed above.To correct for bias introduced by not sampling all 300 lakes, we replaced missing data using multiple imputation (Levy, 1999). Multiple imputation is a technique for estimating the uncertainty of imputed variables. For each variable for each lake not sampled in a given bin, we chose at random (with replacement) a value from lakes sampled in that bin. We repeated the imputation 1000 times to provide a distribution of estimates for each variable in the lakes not sampled. The distribution mean for each variable in each lake was used in the calculation of the median for the regional lake population. We chose to present the median for the 300 lakes because distributions tended to be highly skewed. For comparison purposes, we also calculated the median from sampled lakes only (i.e. excluding imputed data). The mean cumulative distributions for some variables, including 95% confidence intervals, were plotted from the 1000 cumulative distributions generated by multiple imputation.We fit a Pareto distribution to the regional lake area data set to compare the size distribution of NHLD lakes with those of other regions. We used the maximum likelihood estimator for parameter estimates (Bernardo &amp; Smith, 2000). Of particular interest is the parameter (β) that describes the logarithmic decline in number of lakes with lake area, because this parameter has been used previously (Downing et al., 2006, Table 1) to compare lake area distributions among regions and to estimate the global abundance of lakes.Where indicated, results have been area weighted to reflect the influence of lake size. For correlations, data were transformed (log10) to normalise distributions and linearise relationships. Shoreline development factor (SDF), an index of the irregular shape of lakes, was calculated for each lake according to Kalff (2002). The minimum SDF, 1, indicates a lake is a perfect circle.

Methods

DL is used to represent “detection limit” where known.NOTE (1): Each method listed below corresponds with a USGS Parameter Code, which is listed after the variable name. NOTE (2): If the NEMI method # is known, it is also specified at the end of each method description.NOTE (3): Some of the variables are calculated using algorithms within QWDATA. If this is the case see Appendix D of the NWIS User’s Manual for additional information. However, appendix D does not list the algorithm used by the USGS. If a variable is calculated with an algorithm the term: algor, will be listed after the variable name.anc: 99431, Alkalinity is determined in the field by using the gran function plot methods, see TWRI Book 9 Chapter A6.1. anc_1: 90410 and 00410, Alkalinity is determined by titrating the water sample with a standard solution of a strong acid. The end point of the titration is selected as pH 4.5. See USGS TWRI 5-A1/1989, p 57, NEMI method #: I-2030-89.2. c13_c12_ratio: 82081, Exact method unknown. The following method is suspected: Automated dual inlet isotope ratio analysis with sample preparation by precipitation with ammoniacal strontium chloride solution, filtration, purification, acidified of strontium carbonate; sample size is greater than 25 micromoles of carbon; one-sigma uncertainty is approximately ± 0.1 ‰. See USGS Determination of the delta13 C of Dissolved Inorganic Carbon in Water, RSIL Lab Code 1710. Chapter 18 of Section C, Stable Isotope-Ratio Methods Book 10, Methods of the Reston Stable Isotope Laboratory.3. ca, mg, mn, na, and sr all share the same method. The USGS parameter codes are listed first, then the method description with NEMI method #, and finally DL’s:ca- 00915, mg- 00925, mn- 01056, na- 00930, sr- 01080All metals are determined simultaneously on a single sample by a direct reading emission spectrometric method using an inductively coupled argon plasma as an excitation source. Samples are pumped into a crossflow pneumatic nebulizer, and introduced into the plasma through a spray chamber and torch assembly. Each analysis is determined on the basis of the average of three replicate integrations, each of which is background corrected by a spectrum shifting technique except for lithium (670.7 nm) and sodium (589.0 nm). A series of five mixed-element standards and a blank are used for calibration. Method requires an autosampler and emission spectrometry system. See USGS OF 93-125, p 101, NEMI Method #: I-1472-87.DL’s: ca- .02 mg/l, mg-.01 mg/l, mn-1.0 ug/l, na- .2 mg/l, sr- .5 ug/l4. cl, f, and so4 all share the same method. The USGS parameter codes are listed first, then the method description with NEMI method #, and finally DL’s:cl- 00940, f-00950, so4-00945All three anions (chloride, flouride, and sulfate) are separated chromatographically following a single sample injection on an ion exchange column. Ions are separated on the basis of their affinity for the exchange sites of the resin. The separated anions in their acid form are measured using an electrical conductivity cell. Anions are identified on the basis of their retention times compared with known standards. 19 The peak height or area is measured and compared with an analytical curve generated from known standards to quantify the results. See USGS OF 93-125, p 19, NEMI method #: I-2057.DL’s: cl-.2 mg/l, f-.1 mg/l, so4-.2 mg/lco2: 00405, algor, see NWIS User's Manual, QW System, Appendix D, Page 285.co3: 00445, algor.color: 00080, The color of the water is compared to that of the colored glass disks that have been calibrated to correspond to the platinum-cobalt scale of Hazen (1892), See USGS TWRI 5-A1 or1989, P.191, NEMI Method #: I-1250. DL: 1 Pt-Co colorconductance_field: 00094 and 00095, specific conductance is determined in the field using a standard YSI multimeter, See USGS TWRI 9, 6.3.3.A, P. 13, NEMI method #: NFM 6.3.3.A-SW.conductance_lab: 90095, specific conductance is determined by using a wheat and one bridge in which a variable resistance is adjusted so that it is equal to the resistance of the unknown solution between platinized electrodes of a standardized conductivity cell, sample at 25 degrees celcius, See USGS TWRI 5-A1/1989, p 461, NEMI method #: I-1780-85.dic: 00691, This test method can be used to make independent measurements of IC and TC and can also determine TOC as the difference of TC and IC. The basic steps of the procedure are as follows:(1) Removal of IC, if desired, by vacuum degassing;(2) Conversion of remaining inorganic carbon to CO₂ by action of acid in both channels and oxidation of total carbon to CO₂ by action of ultraviolet (UV) radiation in the TC channel. For further information, See ASTM Standards, NEMI method #: D6317. DL: n/adkn: 00623 and 99894, Organic nitrogen compounds are reduced to the ammonium ion by digestion with sulfuric acid in the presence of mercuric sulfate, which acts as a catalyst, and potassium sulfate. The ammonium ion produced by this digestion, as well as the ammonium ion originally present, is determined by reaction with sodium salicylate, sodium nitroprusside, and sodium hypochlorite in an alkaline medium. The resulting color is directly proportional to the concentration of ammonia present, see USGS TWRI 5-A1/1989, p 327, NEMI method #: 351.2. DL: .10 mg/Ldo: 0300, Dissolved oxygen is measured in the field with a standard YSI multimeter, NEMI Method #: NFM 6.2.1-Lum. DL: 1 mg/L.doc: 00681, The sample is acidified, purged to remove carbonates and bicarbonates, and the organic carbon is oxidized to carbon dioxide with persulfate, in the presence of an ultraviolet light. The carbon dioxide is measured by nondispersive infrared spectrometry, see USGS OF 92-480, NEMI Method #: O-1122-92. DL: .10 mg/L.don: 00607, algor, see NWIS User's Manual, QW System, Appendix D, page 291.dp: 00666 and 99893, All forms of phosphorus, including organic phosphorus, are converted to orthophosphate ions using reagents and reaction parameters identical to those used in the block digester procedure for determination of organic nitrogen plus ammonia, that is, sulfuric acid, potassium sulfate, and mercury (II) at a temperature of 370 deg, see USGS OF Report 92-146, or USGS TWRI 5-A1/1979, p 453, NEMI method #: I-2610-91. DL= .012 mg/L.fe: 01046, Iron is determined by atomic absorption spectrometry by direct aspiration of the sample solution into an air-acetylene flame, see USGS TWRI 5-A1/1985, NEMI method #: I-1381. DL= 10µg/L.h_ion: 00191, algor.h20_hardness: 00900, algor.h20_hardness_2: 00902, algor.hco3: 00440, algor.k: 00935, Potassium is determined by atomic absorption spectrometry by direct aspiration of the sample solution into an air-acetylene flame , see USGS TWRI 5-A1/1989, p 393, NEMI method #: I-1630-85. DL= .01 mg/L.n_mixed: 00600, algor.n_mixed_1: 00602, algor.n_mixed_2: 71887, algor.nh3_nh4: 00608, Ammonia reacts with salicylate and hypochlorite ions in the presence of ferricyanide ions to form the salicylic acid analog of indophenol blue (Reardon and others, 1966; Patton and Crouch, 1977; Harfmann and Crouch, 1989). The resulting color is directly proportional to the concentration of ammonia present, See USGS OF 93-125, p 125/1986 (mg/l as N), NEMI Method #: I-2525. DL= .01 mg/L.nh3_nh4_1: 71846, algor.nh3_nh4_2: 00610, same method as 00608, except see USGS TWRI 5-A1/1989, p 321. DL = .01 mg/L.nh3_nh4_3: 71845, algor.no2: 00613, Nitrite ion reacts with sulfanilamide under acidic conditions to form a diazo compound which then couples with N-1-naphthylethylenediamine dihydrochloride to form a red compound, the absorbance of which is measured colorimetrically, see USGS TWRI 5-A1/1989, p 343, NEMI method #: I-2540-90. DL= .01 mg/L.no2_2: 71856, algor.no3: 00618, Nitrate is determined sequentially with six other anions by ion-exchange chromatography, see USGS TWRI 5-A1/1989, P. 339, NEMI method #: I-2057. DL= .05 mg/L.no3_2: 71851, algor.no32: 00630, An acidified sodium chloride extraction procedure is used to extract nitrate and nitrite from samples of bottom material for this determination(Jackson, 1958). Nitrate is reduced to nitrite by cadmium metal. Imidazole is used to buffer the analytical stream. The sample stream then is treated with sulfanilamide to yield a diazo compound, which couples with N-lnaphthylethylenediamine dihydrochloride to form an azo dye, the absorbance of which is measured colorimetrically. Procedure is used to extract nitrate and nitrite from bottom material for this determination (Jackson, 1958), see USGS TWRI 5-A1/1989, p 351. DL= .1 mg/Lno32_2: 00631, same as description for no32, except see USGS OF 93-125, p 157. DL= .1 mg/L.o18_o16_ratio: 82085, Sample preparation by equilibration with carbon dioxide and automated analysis; sample size is 0.1 to 2.0 milliliters of water. For 2-mL samples, the 2-sigma uncertainties of oxygen isotopic measurement results are 0.2 ‰. This means that if the same sample were resubmitted for isotopic analysis, the newly measured value would lie within the uncertainty bounds 95 percent of the time. Water is extracted from soils and plants by distillation with toluene; recommended sample size is 1-5 ml water per analysis, see USGS Determination of the Determination of the delta (18 O or 16O) of Water, RSIL Lab Code 489.o2sat: Dissolved oxygen is measured in the field with a standard YSI multimeter, which also measures % oxygen saturation, NEMI Method #: NFM 6.2.1-Lum.ph_field: 00400, pH determined in situ, using a standard YSI multimeter, see USGS Techniques of Water-Resources Investigations, book 9, Chaps. A1-A9, Chap. A6.4 "pH," NEMI method # NFM 6.4.3.A-SW. DL= .01 pH.ph_lab: 00403, involves use of laboratory pH meter, see USGS TWRI 5-A1/1989, p 363, NEMI method #: I-1586.po4: 00660, algor, see NWIS User's Manual, QW System, Appendix D, Page 286.po4_2: 00671, see USGS TWRI 5-A1/1989, NEMI method #: I-2602. DL= .01 mg/L.s: 63719, cannot determine exact method used. USGS method code: 7704-34-9 is typically used to measure sulfur as a percentage, with an DL =.01 µg/L. It is known that the units for sulfur measurements in this data set are micrograms per liter.sar: 00931, algor, see NWIS User's Manual, QW System, Appendix D, Page 288.si: 00955, Silica reacts with molybdate reagent in acid media to form a yellow silicomolybdate complex. This complex is reduced by ascorbic acid to form the molybdate blue color. The silicomolybdate complex may form either as an alpha or beta polymorph or as a mixture of both. Because the two polymorphic forms have absorbance maxima at different wavelengths, the pH of the mixture is kept below 2.5, a condition that favors formation of the beta polymorph (Govett, 1961; Mullen and Riley, 1955; Strickland, 1952), see USGS TWRI 5-A1/1989, p 417, NEMI method #: I-2700-85. DL= .10 mg/L.spc: 00932, algor, see NWIS User's Manual, QW System, Appendix D, Page 289.tds: 70300 and 70301, A well-mixed sample is filtered through a standard glass fiber filter. The filtrate is evaporated and dried to constant weight at 180 deg C, see " Filterable Residue by Drying Oven," NEMI method #: 160.1, DL= 10 mg/l. Note: despite DL values occur in the data set that are less than 10 mg/l.tds_1: 70301, algor, see NWIS User's Manual, QW System, Appendix D, Page 289.tds_2: 70303, algor, see NWIS User's Manual, QW System, Appendix D, Page 290.tkn: 00625 and 99892, Block digester procedure for determination of organic nitrogen plus ammonia, that is, sulfuric acid, potassium sulfate, and Mercury (II) at a temperature of 370°C. See the USGS Open File Report 92-146 for further details. DL: .10 mg/L.toc: 00680, The sample is acidified, purged to remove carbonates and bicarbonates, and the organic carbon is oxidized to carbon dioxide with persulfate, in the presence of an ultraviolet light. The carbon dioxide is measured by nondispersive infrared spectrometry, see USGS TWRI 5-A3/1987, p 15, NEMI Method #: O-1122-92. DL=.10 mg/L.ton: 00605, algor, See NWIS User's Manual, QW System, Appendix D, page 286.tp: 00665 and 99891, This method may be used to analyze most water, wastewater, brines, and water-suspended sediment containing from 0.01 to 1.0 mg/L of phosphorus. Samples containing greater concentrations need to be diluted, see USGS TWRI 5-A1/1989, p 367, NEMI method #: I-4607. tp_2: 71886, algor.tpc: 00694, The basic steps of this test method are:1) Conversion of remaining IC to CO2 by action of acid, 2) Removal of IC, if desired, by vacuum degassing, 3) Split of flow into two streams to provide for separate IC and TC measurements, 4) Oxidation of TC to CO2 by action of acid-persulfate aided by ultraviolet (UV) radiation in the TC channel, 5) Detection of CO2 by passing each liquid stream over membranes that allow the specific passage of CO2 to high-purity water where change in conductivity is measured, and 6) Conversion of the conductivity detector signal to a display of carbon concentration in parts per million (ppm = mg/L) or parts per billion (ppb = ug/L). The IC channel reading is subtracted from the TC channel reading to give a TOC reading, see ASTM Standards, NEMI Method #: D5997. DL= .06 µg/L.tpn: 49570, A weighed amount of dried particulate (from water) or sediment is combusted at a high temperature using an elemental analyzer. The combustion products are passed over a copper reduction tube to covert nitrogen oxides to molecular nitrogen. Carbon dioxide, nitrogen, and water vapor are mixed at a known volume, temperature, and pressure. The concentrations of nitrogen and carbon are determined using a series of thermal conductivity detectors/traps, measuring in turn by difference hydrogen (as water vapor), carbon (as carbon dioxide), and nitrogen (as molecular nitrogen). Procedures also are provided to differentiate between organic and inorganic carbon, if desired, see USEPA Method 440, NEMI method #: 440. DL= .01 mg/L.

Methods

see abstract for methods used.

Methods

The 1991-1995 chemistry data obtained from the Lachat auto-analyzer. Like the process data, there are up to seven samples per sampling date due to Van Dorn collections across a depth interval according to percent irradiance. Voichick and LeBouton (1994) describe the autoanalyzer procedures in detail.Methods for 1984-1990 were described by Carpenter and Kitchell (1993) and methods for 1991-1997 were described by Carpenter et al. (2001).Carpenter, S.R. and J.F. Kitchell (eds.). 1993. The Trophic Cascade in Lakes. Cambridge University Press, Cambridge, England.Carpenter, S.R., J.J. Cole, J.R. Hodgson, J.F. Kitchell, M.L. Pace,D. Bade, K.L. Cottingham, T.E. Essington, J.N. Houser and D.E. Schindler. 2001. Trophic cascades, nutrients and lake productivity: whole-lake experiments. Ecological Monographs 71: 163-186.Number of sites: 8