Paq proxy was applied on mid and long-chain n-alkanes in order to develop an index to assist in the long-term assessment of changes and exchanges between aquatic communities in estuarine environments as a result of increased saline incursion. New boundaries are proposed according to n-alkanes abundance in the leaves of local mangrove tree species for better definition of emergent aquatic plant end-member. Molecular distribution and δ13C isotopic signatures of n-alkanes were also used to support the parameter. A predominance of odd carbon-numbered long chain (> C27 n-alkanes) indicated a main terrestrial input, although mid-chain n-alkanes (23 and 25 carbons) were also identified. Short-chain n-alkanes (< 19) were absent or found in a very small concentration. Carbon Preference Index and C/N ratio reinforced a terrestrial origin for the sedimentary organic matter. δ13C signatures of n-alkanes for C23, C25, C29 and C31 were characteristic of mangrove input, ranging from -27.57 ‰ (C23) to -34.40 ‰ (C29) for Piraquê-Mirim River (PM) and from -27.36 ‰ (C23) to -32.84 ‰ (C31) for Piraquê-Açu River (PA) without any particular trend. Paq proxy was successfully used to identify rises in marine macrophytes (mid-chain n-alkanes) input mainly in the confluence and PM probably as consequence of drought periods. The confluence presented a mixing sources of OM. PA was identified as a stable mangrove environment while PM was characterized by pulses of marine macrophytes input and should be managed with care in respect to its catchment for water use and dam constructions as a shortage of fresh water can alter the estuarine ecology.
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