The Mahakam Delta is a tropical, fluvio–tidally dominated delta prograding onto a mixed siliciclastic–carbonate shelf. Surface sediments were collected from 12 distinctive depositional environments extending from the head of the Mahakam Delta to the shelf edge. Organic matter was extracted from 200 samples by acid digestion, and seven palynomorph types (pollen, embryophyte spores, fungal spores, foraminiferal linings, copepod eggs, tintinnomorphs, and dinocysts) were identified and counted, and their percentages and concentrations calculated. Total organic carbon (TOC), lithology, and depositional environments were recorded for each sediment sample.

The amounts of terrestrial palynomorphs in sediments can be explained by transport and depositional processes, and four groups of environments are identified (tidally influenced, detrital peat beach, lowland rain forest, and marine shelf). Because of tidal flushing of the delta plain, pollen, embryophyte spores, fungal spores and soft plant debris from the soil litter are deposited together with clastic mud at slack-water periods. As a result, all tidally-influenced environments exhibit constant numbers of pollen, embryophyte spores, and fungal spores per unit of TOC. In lowland rain forest sediments, there is minor clastic dilution and the numbers of pollen and spores are three to 10 times higher per unit TOC than in tidally-influenced sediments. In detrital peat beach and marine shelf sediments, the number of sporomorphs per unit TOC is lower than expected because of the selective removal of sporomorph-sized particles by wave action and of dilution with autochthonous marine organic matter respectively.

In contrast, the amounts of marine palynomorphs in sediments are related to the depositional environments. Relative amounts of marine palynomorphs increase gradually offshore, as both the sporomorph percentages and concentrations decrease simultaneously. Once in fully marine conditions, concentrations of marine palynomorphs are comparable in all shelf environments. The marine assemblages are mainly represented by zooplankton (copepod eggs) and benthic protists (foraminiferal linings), the phytoplanktonic constituent (dinocyst) playing a subordinate role.

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