The exploitation of lakes has led to large-scale contemporary impacts on freshwater systems, largely in response to catchment clearance. Such clearance is causing changes to carbon dynamics in tropical lakes which may have significance for wider carbon budgets, depending on the changes in carbon sequestration and mineralisation driven by changing roles of terrestrial and aquatic carbon in lakes over time. Despite increasing awareness of the pivotal role of carbon source in carbon dynamics, discriminating the source of carbon from a palaeolimnological record is rarely undertaken. Here we use novel geochemical techniques (brGDGTs, n-alkanes, Rock-Eval pyrolysis), paired with traditional analyses (diatoms, pollen), to elucidate changing sources of carbon through time and ecosystem response.Environmental changes at Lake Nyamogusingiri can be divided into three phases: Phase I (CE 1150–1275), a shallow and productive lake, where a diverse terrestrial environment is, initially, the main carbon source, before switching to an aquatic source; Phase II (CE 1275–1900), variable lake levels (generally in decline) with increasing productivity, and carbon is autochthonous in source; Phase III (CE 1900–2007), lake level declines, and the carbon is of a mixed source, though the terrestrially derived carbon is from a less diverse source.The organic geochemical analyses provide a wealth of data regarding the complexity of aquatic response to catchment and with-in lake changes. These data demonstrate that small, tropical lake systems have the potential to bury high quantities of carbon, which has implications for the disruption of local biogeochemical cycles (C, P, N, and Si) both in the past, and the future as human and climate pressures increase.
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