Supplementary Materials

Bacterioplankton community sampling and fingerprinting

121 bacterioplankton community (BC) samples were collected from the
integrated upper water column (0-12m) on monthly- to twice-monthly basis
from 2000-2009 under ice-free conditions on Lake Mendota, Wisconsin, USA.
Sample dates are listed in Supplementary Table 1 (S1). Samples were
collected from the location of maximum depth in Lake Mendota at 43 06 N,
89 24W, 327 m.s.l. Seasons were defined by the astronomical March and
September equinox and the June solstice.
Samples were filtered (0.2 m Pall Supor filters) and stored at -80 C
until subsequent processing. Deoxyribonucleic acid (DNA) was extracted with
QBiogene Bio101 FastDNA extraction kit and modifications to manufacturers
protocol described previously (Yannarell et al., 2003; Yannarell & Triplett,
2005), and followed by amplification by polymerase chain reaction and
automated ribosomal intergenic spacer analysis (ARISA) as described by
Shade and colleagues (Shade et al., 2007). ARISA profiles were analyzed
using Genemarker v 1.5 software (SoftGenetics, LLC) and a custom R script
developed in the R statistics package (R Development Core Team, 2011) to
aid in high-throughput binning of peaks, as previously described (Jones &
McMahon, 2009).
Environmental variables
Thirty-three physical, chemical and biological water quality parameters
were collected at biweekly frequency during ice-free seasons by the North
Temperate Lakes Long Term Ecological Research (NTL LTER) program at the
same location as microbial sample collection; a complete listing of variables,
protocols, and observational data is available at www.lter.limnology.wisc.edu
and variables and abbreviations are listed in Supplementary Tables 1 and 2
(NTL-LTER, 2011a, 2011b, 2011c). Data underwent quality control as
described in NTL LTER protocols, all flagged data were removed, and

replicates averaged. Phytoplankton samples were collected across a

vertically averaged integrated depth 0-8m and biomass was summed at the
division level for functional groups Cyanophyta, Bacillariophyta, and
Chlorophyta. For zooplankton, organism density was used. For all other
variables, discrete depth measurements were typically made every 1-4 m
from 0-20 m depth; all variables measured between 0-12m depths were
vertically-averaged.
When NTL LTER observations did not co-occur with microbial sampling,
time-weighted averages of observations within +/- 17 days were assigned to
microbial observations. For >90% of samples, LTER environmental
observations occurred within 7 days of bacterioplankton sampling. For timeweighted interpolation, nearby observations were averaged after being
weighted by a value inversely proportional the absolute value of the number
of days between water quality observations and microbial observations:
Yint = [ni=1 wi *yi] / ni=1 wi
wi= 17-|xi-x0|
Where Yint is the interpolated value used in subsequent analyses for microbial
samples corresponding to day of year x0, n is the number of observations
made within +/- 17 days of x0 for any given year, xi is day of year that
variable yi was collected on. wi is the weighted factor which is proportional
to the temporal proximity of the water quality observation to the microbial
observation. For example: a microbial sample was collected on day 50 (x0 =
50), and NTL LTER water quality samples were collected on day 40 (x1) and
54 (x2). If temperature is unknown on day 50, but had values of 15 (y1) and
18 (y2),
Yint = [((17-|40-50|)*15)+ ((17-|54-50|)*18)] / ((17-|40-50|) +(17-|54-50|)) =
17.0

Table S1. Bacterioplankton community sampling dates

Microbial sampling dates (mm/dd/yy)
3/15/00
3/30/00
4/14/00
4/27/00
5/11/00
6/6/00
6/20/00
7/17/00
8/1/00
8/17/00
9/12/00
9/26/00
10/10/00
10/24/00
11/28/00
3/13/01
4/23/01
5/21/01
6/4/01
7/2/01
7/5/01
7/16/01
7/30/01
8/13/01
8/28/01
9/10/01
9/26/01
10/20/01
11/6/01
11/26/01
5/24/02
7/1/02
8/1/02

8/29/02
9/12/02
9/24/02
10/8/02
10/22/02
11/7/02
11/20/02
5/13/03
5/28/03
6/9/03
6/27/03
7/23/03
8/7/03
9/8/03
9/22/03
10/15/03
11/11/03
5/19/04
5/26/04
6/11/04
6/25/04
7/8/04
7/22/04
9/2/04
9/16/04
9/30/04
10/12/04
9/16/04
9/30/04
10/12/04
4/11/05
5/25/05
6/22/05

8/2/05
8/19/05
8/31/05
9/18/05
10/10/05
11/8/05
4/6/06
4/21/06
5/4/06
5/15/06
6/9/06
7/13/06
7/17/06
8/3/06
8/22/06
9/8/06
10/6/06
10/20/06
11/3/06
11/16/06
5/11/07
5/29/07
6/11/07
7/23/07
8/6/07
8/20/07
9/27/07
10/12/07
11/1/07
5/10/08
6/5/08
6/25/08
7/11/08

7/22/08
8/7/08
8/22/08
9/5/08
9/15/08
10/2/08
10/17/08
2/24/09
4/29/09
6/9/09
6/18/09
6/26/09
7/7/09
7/30/09
8/10/09
8/26/09
9/13/09
9/27/09
10/9/09
10/26/09
11/14/09
12/4/09

Table S2. Environmental variables and abbreviations

Environmental variables
Month
Year
Day of year
Day length
Alkalinity
Calcium
Chlorophyll-a
Chloride
Dissolved inorganic carbon
Dissolved oxygen
Dissolved organic carbon
Dissolved oxygen percent

Abbreviation
Month
Year
Day of year
Day Length
Alk
Ca
Chl
Cl
DIC
DO
DOC
DOsat

saturation
Dissolved reactive silica

DRSilica

Iron
Potassium
Magnesium
Manganese
Ammonium
Nitrate+ nitrite
Sodium
Sulfate
Soluble reactive phosphorus
Total inorganic carbon
Total kjeldhal nitrogen
Total organic carbon
Total phosphorus
Temperature
Zooplankton density
pH
Secchi depth
Bacillariophyta biomass
Chlorophyta biomass
Cyanophyta biomass

Fe
K
Mg
Mn
NH4
NO3NO2
Na
So4
SRP
TIC
TKN
TOC
TP
Temp
Zoop
pH
Secchi
Bacillarophyta
Chlorophyta
Cyanophyta

Figure S1 Co-occurrence network properties for a ten-year time series of environmental

variables in Lake Mendota, WI, USA (number of nodes (S), edges (L), clustering coefficient
(Cl), and characteristic path length (D)). Open circles indicate properties calculated for
networks that include all observations for a given season. Boxplots represent observationnormalized results: we performed LSA (LSA R > 0.3, p < 0.001, no time lag) and network
analysis on networks generated from Monte Carlo simulations of 30 randomly drawn
observations from each season. Results of 1000 simulations for each season were
aggregated and compared to test the effect on network properties of the number of
observations included in the analysis. Boxes represent inter-quartile range and whiskers
indicate 10th and 90th percentiles, red pluses indicate outliers. Significant differences exist
between observation-normalized distributions of network properties from each season, for
all properties (Wilcoxon rank sum test: =0.01, p<0.0001).

Figure S2 Box and whisker plots of co-occurrence network properties using same bootstrapping technique as described in main
text, but with a range the correlative local similarity score (R values): 0.1 (upper plots) and 0.5 (lower plots). Plus signs indicate
outliers, while boxes represent 10th and 90th percentiles, and median values. Network trends in clustering coefficient and
average path length reported in text (decreasing cluster coefficient and increasing path length) were generally found in this

sensitivity analysis. One exception to these trends is the average path length for seasonal distributions with higher (0.5) R-value
(L-score).

Citations
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Long Term Ecological Research Program. Madison, WI. Retrieved from
http://www.lternet.edu/sites/ntl/
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