Sediment cores and samples of riverbed and suspended sediments collected from Xingu, Tapajós and Amazon rivers are presented in Figure 1 and in Supplementary Material (Table S1). Suspended sediment samples were taken both during the dry and wet seasons from Xingu, Tapajós, and Amazon rivers in order to fully encompass variations in sediment composition related to hydrological changes. Suspended and riverbed sediment samples from the Amazon mainstem were collected upstream and downstream the Tapajós and Xingu rivers mouths (Figure 1) in order to evaluate the effect of input of sediments from the Xingu and Tapajós rivers on the Amazon River. Suspended sediment samples were collected through water pumped at approximately 60% of the water depth in the channel thalweg. For each sample, four liters of water were filtrated using cellulose acetate membranes (pore size of 0.45 μm). Riverbed sediments were collected using a Van Veen grab sampler. A total of 23 suspended sediment samples and 28 riverbed sediment samples were used in this study.

Sediment cores of the Xingu Ria were collected from deeper portions of the lake-like channel covered by muddy sediments (named “XC”) and from islands in the upstream section of the Xingu Ria (named “EMB”). The locations were selected based on water depth profiles and riverbed sediment sampling (further details in Sawakuchi et al., 2015). Underwater sediment cores from the Xingu Ria channel were retrieved by divers using PVC tubes of up to 6 m in length and percussion method (Sawakuchi et al., 2015). Three underwater sediment cores, characterized by dark gray to brown muds with thicknesses of 300 cm (XC02), 370 cm (XC03), and 470 cm (XC05), respectively, were retrieved from the Xingu Ria. Unconsolidated sediments from islands of the Xingu Ria head were collected using a piston-corer attached to a manual auger. Four sediment cores composed of fine to medium sands and muddy organic sediments were obtained from the islands: EMB13-07 (555 cm), EMB13-13 (430 cm), EMB13-17 (250 cm), and EMB13-21 (345 cm). Samples for luminescence dating were collected using opaque plastic tubes.

Bathymetric profiles were recorded along the upstream part of the Xingu Ria using sonar and GPS equipment. Samples collected with the Van Veen grab sampler were used to characterize riverbed sediments along bathymetric profiles. Water depth profiles and texture of riverbed sediments of the Xingu Ria are shown in Figure 2.

Total organic carbon (TOC) content and its stable carbon isotope ratios (δ¹³C_org) were measured in 28 riverbed sediments samples at MARUM, University of Bremen. Sediments from the core XC05 were sampled at 2 cm intervals for total carbon coulometric and x-ray fluorescence (XRF) analysis at the University of Kentucky.

Major elements (P, Ca, Fe, Mn, Al, Ti, K) concentrations were determined with an Agilent 720 inductively coupled plasma—optical emission spectrometer (ICP-OES) for 23 samples of suspended sediments and with a Bruker Tracer IV SD energy dispersive x-ray fluorescence (XRF) spectrometer for 13 riverbed sediments samples and 234 samples of the sediment core XC05. ICP-OES analysis of suspended sediments and XRF analysis of riverbed sediments were performed at MARUM, University of Bremen. For ICP-OES analysis, digestion of suspended material was performed with a MLS 1200 MEGA microwave system. For this purpose, 7 ml HNO₃ (65%), 0.5 ml HF (40%), 0.5 ml HCl (30%), and 0.5 ml MilliQ were added to about 50 mg sample material (filter plus suspended material) previously placed into Teflon liners. All acids were of supra-pure quality. For XRF analysis, sediments were prepared by freeze drying, grinding by hand with an agate mortar and pestle, and sieving to ~125 μm prior to packing into inert sample boats sealed with an ultra-thin mylar window. Individual XRF scans for each sample were made through the mylar window over 90 s, in order to maximize signal-to-noise. Major elements (atomic numbers 11 through 30) were collected under a ~9 torr vacuum, by setting the XRF filter to 15 keV and 35 μA. Trace elements (atomic numbers 20 through 51), were collected at 40 keV and 15 μA without a vacuum. Calibration of unknowns utilized Bruker proprietary software (S1CALPROCESS with TR2.cfz and MA1.cfz) and a reference catalog of mudrock chemistry described in Rowe et al. (2012). Internal consistency of the XRF was verified by routine scanning of the SARM41 shale standard (Ring, 1989). The chief focus of our analysis was the major rock-forming (Al, Ca, K, Ti, P) and redox-sensitive (Mn, Fe) elements. Inorganic chemistry data provide insights on mineralogy as well as depositional environments and hydrodynamic processes, especially when paired with organic carbon data (Sageman et al., 2003; Algeo and Rowe, 2012; Scott and Lyons, 2012).

Total organic carbon (TOC) was determined using a LECO CS 200 CS-Analyzing System and an UIC Coulometrics Inc. Carbonate Coulometer (Engleman et al., 1985). The LECO method determines total carbon content through combustion of a powdered sample (Jarvie, 1991). Values of TOC were obtained by subtracting total inorganic carbon determined by the coulometer from total carbon. This method is routinely employed in paleoenvironmental analysis due to its accuracy and small sample size requirements (Jackson and Roof, 1992; Schulte et al., 2000; e.g., Böning et al., 2005). The precision of the analysis, based on analysis of internal standards and replicates, was typically better than ± 0.15%. The δ¹³C_org signature of de-carbonated samples was analyzed on a Finnigan MAT Delta plus coupled to a CE elemental analyzer. δ¹³C_org is reported using the delta notation relative to the Vienna Pee Dee Belemnite (VPDB). The uncertainty was less than ± 0.1‰.

Results were analyzed using R software (R Core Team, 2015). Major changes in hydrology and paleoenvironmental conditions were determined using constrained hierarchical cluster analysis of geochemistry and magnetic susceptibility data by the method of incremental sum of squares (CONISS, Grimm, 1987).

Magnetic susceptibility measurements were performed at the Paleomagnetic Laboratory (USPMag) of the Institute of Astronomy, Geophysics and Atmospheric Sciences of the University of São Paulo (IAG/USP). Magnetic susceptibility is used here as a complimentary method to identify significant variations in paleoenvironmental conditions or sediment composition in core XC05. A total of 194 paleomagnetic specimens were collected from the sediment core using cubic plastic boxes (8 cm³) placed side-by-side throughout the core. Low-field magnetic susceptibility of individual specimen was measured using a Kappabridge MFK1-FA system (AGICO Ltd). Two different frequencies (976 and 15616 Hz) were used in a 200 Am⁻¹ field at room temperature (Dearing et al., 1996). All data were mass normalized due to the irregular sample mass inside cubic boxes.

Riverbed samples were subsampled for pollen analyses (Table S1). Samples were processed for extraction of pollen grains using the protocol established by Colinvaux et al. (1999). The analyses were performed in the Institute of Geosciences of the University of São Paulo (IGc/USP) under a microscope with magnification of 600x. A minimum of 300 terrestrial pollen grains were counted per sample. Aquatic taxa and spores are not included in the sum of pollen assemblage. The pollen grains and spores were identified using the pollen reference collection of the University of São Paulo and other published reference materials (Erdtman, 1952; Roubik and Moreno, 1991; Colinvaux et al., 1999). The raw pollen count data were entered into the Tilia software (Grimm, 2011), in order to calculate the taxa percentages and concentrations.

Riverbed and sediment core XC05 were subsampled for diatom analyses. Diatom analysis followed standard procedures discussed by Battarbee et al. (2001). Slides were mounted with Naphrax® as medium. Optical observations and counts were conducted at a magnification of 1000x with a Zeiss Axioskop 2 plus microscope. At least 400 valves were counted per slide. Taxonomy and nomenclature followed published literature sources (e.g., Round et al., 1990; Krammer, 2000; Rumrich et al., 2000; Metzeltin and Lange-Bertalot, 2007) and the on-line catalog of valid names (California Academy of Sciences, 2011).

Sediment core XC05 was sub-sampled in field on the same day of collection for the assessment of dissolved methane and carbon dioxide concentrations in pore waters. Aliquots of 5 ml of wet sediment were collected with an open-ended 5 ml polypropylene syringe after carefully drilling holes at 10 cm intervals. Immediately after collection, the aliquots were injected into a 120 ml vial containing 10 ml of NaOH (5%), capped with butyl rubber stoppers and sealed with aluminum crimps. Control standards of ambient air were collected during sampling for corrections. In the Center for Nuclear Energy in Agriculture of the University of São Paulo (CENA/USP), samples were shaken for headspace equilibration and 60 ml of gas sample was retrieved from vials headspace using a 60 ml syringe and analyzed by Cavity Ring Down Spectroscopy using a Picarro G2201-i device. Samples were slowly injected following the pump flow, taking care not to change the internal pressure, which can be monitored by the analyzer. The 60 ml analyzes took approximately 3 min to pass through the analyzer giving a steady measurement for roughly 40 s that was checked with three standard gas mixtures for concentration and carbon isotope composition of CH₄. Reproducibility between replicates presented a variation of the standard deviation >0.5% for concentration and >0.9% for δ¹³C_CH4. Readings of concentration (ppm) and δ¹³C_CH4 (‰) by the analyzer were slightly different than the standard reference values. Thus, sample results were corrected according to a standard calibration curve.

Optically stimulated luminescence (OSL) dating was carried out in fine silt or sand quartz aliquots from cores XC02, XC03, and XC05 in the Luminescence and Gamma Spectrometry Laboratory of the IGc/USP. Quartz aliquots for luminescence measurements were prepared under subdued red light. Wet sieving and settling procedures were used to isolate the 4–11 or 180–250 μm grain sizes. The target grain size fractions were submitted to oxygen peroxide (H₂O₂) and hydrochloric (HCl 10%) treatments to remove organic matter and carbonates, respectively. Heavy liquid separation of quartz sand grains was performed using lithium metatungstate solution at densities of 2.75 and 2.62 g cm⁻³ to remove heavy minerals and feldspar grains, respectively. Concentrates of quartz sand grains were etched with hydrofluoric acid (HF 38%) for 40 min in order to remove the outer rind of quartz grains damaged by alpha particles and remnant feldspar grains. Luminescence measurements were performed in two automated Risø OSL/TL reader model DA-20 equipped with blue (470 nm) and infrared (870 nm) LEDs for light stimulation, Hoya U-340 filter for light detection in the ultraviolet band and built-in beta radiation sources (⁹⁰Sr/⁹⁰Y) delivering dose rates of 0.088 and 0.135 Gy s⁻¹ (for aluminum discs). Equivalent doses were determined through the single-aliquot regenerative dose protocol (Murray and Wintle, 2000). For fine silt, a mean a-value of 0.04 was considered for calculation of alpha dose rate in quartz. Tests with infrared stimulation indicated absence of feldspar in the fine silt concentrates. A dose recovery test was performed to set up the luminescence measurements protocol to the studied samples batch. Samples equivalent doses were calculated through the Central Age Model (Galbraith et al., 1999). The concentrations of K, ²³⁸U and ²³²Th for dose rate calculations were determined using high resolution gamma spectrometry with a high purity germanium detector (relative efficiency of 55% and energy resolution of 2.1 KeV) encased in an ultralow background shield. Samples were packed in sealed plastic containers and stored for at least 28 days for radon equilibration before gamma spectrometry. Radiation dose rates were calculated using conversion factors outlined by Guérin et al. (2011). Radiation dose rates were corrected for water saturation (water weight/dry sample weight). Cosmic dose rates were calculated through samples latitude, longitude, elevation and burial depth, according to Prescott and Hutton (1994).

Accelerator mass spectrometry (AMS) radiocarbon (¹⁴C) dating was performed on leaves and charcoal fragments retrieved from the sediment cores. Samples were treated in the Radiocarbon Laboratory of the Illinois State Geological Survey and submitted to the Keck Carbon Cycle AMS Laboratory of the University of California-Irvine for AMS ¹⁴C analysis. The ¹⁴C dates were calibrated using the program Calib 7.0 and the calibration curve IntCal 13 (Stuiver and Reimer, 1993; Reimer et al., 2013).

Geochemical results are summarized in Tables 1, 2 (discretized dataset in Table S1). Strong variations in suspended sediment composition were identified between wet and dry seasons in the Xingu, Tapajós, and Amazon rivers (Table 1, Figure 3). Seasonal changes in suspended sediments of the Xingu and Tapajós rivers include the increase in the relative amount of P in sediments of the dry season, which is directly related to primary productivity (Engstrom and Wright, 1984; Dean and Gorham, 1998). The P/Ti ratio is an effective proxy to evaluate the sedimentation of phosphorous regardless of terrigenous input and it avoids dilution effects caused by changes in sedimentation rate (Latimer and Filippelli, 2002; Filippelli et al., 2003). Average P/Ti ratios in the Xingu River vary from 0.66 in the wet season to 4.20 in the dry season. Seasonal changes in P concentration have lower amplitudes in the Tapajós River, with the P/Ti ratio shifting from 0.75 to 0.94 from the wet to the dry seasons, respectively. The Fe/K ratio is a useful indicator of mineralogical stability, since the most stable rock-forming minerals have lower Fe/K ratios (K-feldspar, muscovite, and quartz) and unstable minerals tend to be richer in iron content (Herron, 1988; Armstrong-Altrin and Machain-Castillo, 2016). Fe/K ratios increase during the wet season both in the Xingu and Tapajós rivers, with relatively little variation in the Amazon River (Table 3). In the Xingu River, Ca concentrations increase from 0.09 to 0.35 mg l⁻¹ and P concentration from 0.03 to 0.71 mg l⁻¹ between the wet and dry season. Fe concentrations shift from 1.11 to 2.56 mg l⁻¹ from the wet to the dry season. The inverse pattern is observed in the Amazon River, with Ca, P, and Fe concentrations decreasing in the dry season (Table 1, Figure 3). In the Tapajós River, these shifts between wet and dry seasons have lower amplitude, with Ca concentration varying from 0.07 to 0.13 mg l⁻¹, P varying from 0.03 to 0.05 mg l⁻¹ and Fe varying from 0.99 to 0.76 mg l⁻¹.

In total, 45 pollen taxa were identified in riverbed sediments of the Xingu Ria (Figures S1–S4). The vegetation represented by pollen retrieved from riverbed sediments has great diversity and high percentages of forest elements. Arboreal taxa encountered in the samples include Acalypha, Alchornea, Annacardiaceae, Apocynaceae, Arecaceae, Attalea, Bignoniaceae, Cecropia, Combretum, Dalbergia, Didymopanax, Euterpe, Fabacea, Genipa, Machaerium, Mauritia, Mauritiella, Matayba, Melastomataceae, Mimosa, Myrtaceae, Palmae, Psidium, Psychotria, Sapium, Spondias, Sterculiaceae, Stigmaphyllon, Talisia, and Zygia. Terrestrial herbaceous elements are represented by Alternanthera, Asteraceae, Bambusa, Begonia, Caesaria, Lamiaceae, Phyllanthus, Pilea, Poaceae, Polygonaceae and Symmeria. Sagitaria, Cyperaceae, Alismataceae represent taxa of aquatic herbs. Spores identified in the analysis include Polypodiaceae, trilete and Monolete. The palynologic data indicate that riverbed sediments of the Xingu Ria record the input of sediments from areas where the predominant vegetation type is forest (Figure S5).

Regarding the diatoms, a total of 65 infrageneric taxa were identified in riverbed sediments of the Xingu Ria. Eunotia and Gomphonema were the most represented genera regarding species number (24.6% of total species), followed by genus Aulacoseira (9.2%) (Figure S6). Eunotia species are mostly acidophilic, oligotrophic, and typified by a dominant periphytic habitat (Round et al., 1990; van Dam et al., 1994; Moro and Fürstenberger, 1997; Hamilton and Siver, 2010). Due to the secretion of mucilage by the apical pore fields, Gomphonema is a common genus in periphytic algal communities, being well represented in richness and density (Tremarin et al., 2009). Aulacoseira is a common planktonic genus inhabiting lacustrine and running freshwaters, developing in various trophic conditions (Denys et al., 2003; Zalat and Vildary, 2007). Ecological information at species level is required to use this genus as indicator of water quality (Bicudo et al., 2016).

Diatoms presented well-preserved frustules throughout the core. Assemblages from the core XC05 base showed little variation among genera, and besides the planktonic genus Aulacoseira, comprised benthic and periphytic genera that require surfaces for developing (e.g., Eunotia, Pinnularia and Surirella), suggesting a water column under acidic and oligotrophic conditions with high light penetration. Genera Surirella, Diploneis, Aulacoseira, Placoneis, Gomphonema, Encyonema, and Eunotia were observed throughout the core, suggesting a relatively uniform slack water environment.

Sediments of the three studied underwater cores (XC02, XC03, and XC05) are composed of dark gray to brown organic-rich muddy sediments. As highlighted in Figure 2, these sediments are similar to the modern surface sediments that accumulate in most of the rias. Samples from the top and bottom of sediment cores XC02 (10–293 cm), XC03 (10–363 cm) and XC05 (45–440 cm) were collected for OSL dating. The luminescence ages of cores XC02, XC03, and XC05 ranged from 118 ± 81 to 4,086 ± 159 years (Table 4), suggesting that the Xingu Ria is a slack water environment acting as trap of fine-grained sediments at least since the middle Holocene. XC02 sediments showed ages from 2,503 ± 462 to 3,295 ± 542 years. XC03 and XC05 sediments cover periods from 118 ± 81 to 1,251 ± 211 years, and from 3,025 ± 185 to 4,086 ± 159 years, respectively. Sediment depth profiles described in the islands of the head of the Xingu Ria (EMB13-07, EMB13-13 and EMB13-17) show dark gray organic-rich sediments interlayered with sands and light gray floodplain sediments (Figure 4). Radiocarbon ages obtained in the dark gray muds, which likely represent buried ria sediments, varied from 141–267 to 5,479–5,580 cal years BP (Table 5, Figure 4).

Luminescence and radiocarbon ages allowed the calculation of sedimentation rates for the organic-rich sediments of the Xingu Ria. In the Xingu Ria, sedimentation rates calculated through luminescence ages of core XC05 varied between 0.27 cm yr⁻¹ and 0.70 cm yr⁻¹ (average of 0.37 cm yr⁻¹). The rate of deposition of core XC05 increases from about 0.28 cm yr⁻¹ during the period of ~4,100 to ~3,300 years ago to an average of 0.60 cm yr⁻¹ during the period of ~3,300 to ~3,000 years ago. Cores XC02 and XC03 presented average sedimentation rates of 0.36 cm yr⁻¹ and 0.31 cm yr⁻¹, respectively. Sedimentation rates for organic-rich sediments underneath floodplain sediments of the Xingu Ria head were 0.24 cm yr⁻¹, 0.78 cm yr⁻¹, 0.05 cm yr⁻¹ in profiles EMB13-07, EMB13-13 and EMB13-17, respectively (Figure 4). In the Tapajós Ria, sedimentation rates were calculated through radiocarbon ages presented in Irion et al. (2006). Rates of sediment deposition in the Tapajós Ria vary from 0.24 cm yr⁻¹ to 0.65 cm yr⁻¹ (average of 0.37 cm yr⁻¹).

Magnetic susceptibility measurements were performed on the XC05 core. Low-field magnetic susceptibility varies from 3.4 × 10⁻⁸ to 1.9 × 10⁻⁷ m³kg⁻¹ (Figure 5). Strong magnetic susceptibility variations (peaks) may indicate variations in sedimentation rate or increased magnetic mineral concentrations. The dendogram of geochemical data demonstrates abrupt shifts in the compositional similarity of sediments deposited at 3,690–3,650, 3,345–3,335, and 3,235–3,240 years ago. These shifts fit well with peaks in magnetic susceptibility and P, Fe, Mn, and TIC concentration as well as with the decrease in TOC and lithophilic elements (Figure 5).

Ti concentration reveals significant positive correlations with Al (r = 0.81, n = 198) and K (r = 0.75, n = 198). These elements were used as proxies for the relative contribution of terrigenous sediment input from the Xingu River to the downstream Xingu Ria lake (Engstrom and Wright, 1984; Boës et al., 2011). Results show significant inverse correlation among P concentration and lithophilic elements represented by Ti (r = −0.31, n = 198), Al (r = −0.32, n = 198) and K (r = −0.46, n = 198). P concentration also shows significant positive correlations with Fe (r = 0.57, 198), TIC (r = 0.51, n = 198) and Mn (r = 0.51, n = 198).

Total organic carbon (TOC) concentration varies between 1.77 and 3.35% (average of 2.45%) in sediment core XC05. The measured concentrations are similar to values in samples from bottom sediments of the Xingu Ria (Häggi et al., 2016). Values of δ¹³C_org range from −31.04 to −27.49‰, and indicate that organic matter from bottom sediments of the Xingu Ria is mainly derived from arboreal C3 vegetation (Table S1). This is supported by palynological data, with pollen assemblages dominated by forest taxa (Figure S1).

CH₄ concentrations in pore waters reach values up to 25% (volume) in XC05 sediment core (Figure 5). The values of δ¹³C_CH4 in pore waters of XC05 core range from −71 to −57‰ PDB. Higher (more positive) values of δ¹³C_CH4 often agree with peaks in magnetic susceptibility, Fe concentration and P/Ti (Figure 5). This suggests that CH₄ oxidation in pore waters might increase during drier periods.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.