Supplementary Information Materials and Methods

Sediment sampling and treatment Washington Lake (WL): Three sediment cores from the deepest basin were analyzed: one 85 cm long sediment-water interface core (WL2-MW2) and two long cores (WL1 and WL2) that penetrated to the coral basement at 9.3 and 7.3 m, respectively (Fig. 2). Sedimentation began around 1200 B.C. (Table S1). Sequential core sections (100 cm each) were obtained with a Livingstone-type rod-operated piston corer (Geocore, Columbus, Ohio), sealed in the field and kept refrigerated at 4°C until core splitting, imaging and sub-sampling. This coring device was adapted to fit a transparent PVC tube (54 mm OD) and a custom-made rubber piston allowing intact recovery of the fragile uppermost part of the sediment-water interface. The same device was used in each of the three locations in this study. Sediment-water interface cores were subsampled on site in 1 cm intervals and frozen the same day. Christmas Island (CI): Lake F6 (1°51 ' 5' ' N, 157°24 ' 34' ' W; surface area 0.16 km 2) showed little chemical or physical variation through the 6.1 m-deep water column 1. A 92 cm surface core was recovered that contained thick, red, gelatinous, living microbial mat and the underlying buried mat material (Fig. 2k). An intact mat was recovered by hand and sampled into visually distinct color layers for microscopy (Fig. 2l,m,n). Spooky Lake, Palau (SL): a sediment-water interface core was recovered from the center of the eastern-most basin in 12 m of water. El Junco, Galápagos (EJ): Sediments used in this study are from a sediment-water interface core (EJ7-MW1) recovered from the center of the lake, and from a nearby 3.5 m core obtained with a 2 nature geoscience | www.nature.com/naturegeoscienc