Supplementary Figure 1. Distribution of the study lakes across Sweden.
Supplementary Figure 2. Multivariate analysis of molecular data and landscape and climatic drivers using non-metric multidimensional scaling. Ordinations are based on either Bray-Curtis (a; stress=0.0966), which utilizes relative peak abundances, or Jaccard distances (b; stress=0.1143), which utilizes presence/absence information. Only landscape and climate variables were fit to the NMDS ordination; for an NMDS including water chemistry variables see Figure 2. Gray shaded circles are DOM compounds, whereas black circles indicate the site. Variables with a significance level of < 0.05 (light blue), < 0.01 (green), and < 0.001 (purple) are shown. P-values were calculated over 999 permutations. WRT, water residence time; MAP, mean annual precipitation; MAT, mean annual temperature. 2
Supplementary Figure 3. Molecular-level DOM dynamics of 981 core molecules across 120 Swedish lakes. Only molecular formulae that occur in at least 90% of the lakes were considered, as opposed to molecular formulae occurring in at least three samples (Figure 3). Significant Spearman rank correlation coefficients (p-value < 0.02674) of individual molecules with (a) mean annual precipitation, (b) water residence time, (c) mean annual temperature, and (d) the chemodiversity index. The color indicates molecular-level correlations between the intensity of individual molecules and mean annual precipitation, water residence time, mean annual temperature, and chemodiversity index. Circles and diamonds indicate N-free and N- containing compounds, respectively. The number of positive and negative significant correlations can be found in Supplementary Table 2. 3
H/C 1.5 Aliphatic Highly unsaturated and phenolic compounds 1.0 Vascular plantderived polyphenols n 0.5 CHO CHON CHOS Combustio - der i ved polycyclic aromates n=981 0.0 0.2 0.4 0.6 0.8 1.0 O/C Supplementary Figure 4. Molecular composition of peaks included in Spearman rank correlation coefficient analyses. Molecules were included in the constrained analyses if they were in at least 90% of samples and at least half the samples had a value greater than the dataset detection limit (n = 981). Light blue dots contain nitrogen, and purple dots contain sulphur. 4
Variable Median Range Mean annual precipitation (mm) 650 450-1150 Mean annual temperature ( C) 4.2-5.2-7.5 Growing degree days (days) 190 110-210 Elevation (m) 140 0-740 % Agriculture 1.7 0-64 % Forest 62 3.6-99 % Wetland 9.4 0-68 % Water 6.7 0-29 % Other 8.2 0-77 Slope ( ) 6 1-32 Surface area (km 2 ) <1 <1-136 Runoff (l s -1 ) 56 0-500,000 Water residence time (days) 230 1-2000 Lake/catchment area 0.11 0.056-0.53 Volume (1000 m 3 ) 1100 25-2,200,000 Dissolved organic carbon (mg l -1 ) 11.6 2.40-51.3 Total nitrogen (µg l -1 ) Total organic nitrogen (µg l -1 ) 550 440 100-3500 85-2600 NO 2 + NO 3 (µg l -1 ) 28 1-730 Total phosphorus (µg l -1 ) Total organic phosphorus (µg l -1 ) 14 11 2-370 < 1-270 PO 4 (µg l -1 ) 110 1-230 NH 4 (µg l -1 ) 23 3-480 Chemodiversity index 4803 3418-6398 ph 6.78 4.59-8.07 Conductivity (ms m -1 ) 5.1 0.44-51 Alkalinity (meq l -1 ) 0.16 0-3.0 2- SO 4 (meq l -1 ) 0.072 0.004-1.8 Al (µg l -1 ) 110 10-5300 As (µg l -1 ) 0.4 0.04-7 Ca (meq l -1 ) 0.21 0.008-0.974 Cd (µg l -1 ) 0.015 0.005-0.853 Cl (meq l -1 ) 0.098 0.006-1.012 Co (µg l -1 ) 0.13 0.014-6.11 Cr (µg l -1 ) 0.17 0.05-2.9 Cu (µg l -1 ) 0.51 0.07-6.9 F (mg l -1 ) 0.14 0.03-0.75 Fe (µg l -1 ) 580 14-12000 K (meq l -1 ) 0.017 0.001-0.147 Mg (meq l -1 ) 0.087 0.008-0.974 Mn (µg l -1 ) 40 3-370 Na (meq l -1 ) 0.13 0.14-1.093 Ni (µg l -1 ) 0.46 0.08-6.9 Pb (µg l -1 ) 0.20 0.02-28 Si (mg l -1 ) 2.1 0.02-10 V (µg l -1 ) 0.31 0.03-12 Zn (µg l -1 ) 2.2 0.29-88 Supplementary Table 1. Medians and ranges of environmental and chemical variables, and molecular diversity in lakes across Sweden. 5
Figure 3 Figure 4 (photolabile) Figure 4 (photoresistant) Supplementary Figure 3 Pos/neg Pos/neg Pos/neg Pos/neg Mean annual 507/362 221/14 28/197 359/213 precipitation Water residence time 383/657 25/279 135/21 238/357 Mean annual 698/538 82/127 63/143 282/292 temperature Chemodiversity index 852/435 N/A N/A 315/406 Supplementary Table 2. Number of significant positive and negative correlations in Figures 3 & 4 and Supplementary Figure 3. 6