Erosion regime controls sediment environmental DNA-based community reconstruction

Analysis of environmental DNA detected in lake sediments shows promise to become a great paleoecological technique that can provide detailed information about organism communities living in past environments. However, when interpreting sedimentary environmental DNA records, it is of crucial importance to separate ecosystem responses to large-scale environmental change from “noise” caused by changes in sediment provenance or potential post-depositional DNA mobility. In this study, we show that plant and mammalian communities reconstructed from sediments are strongly affected by sediment provenance, but unaffected by vertical mobility of DNA after sediment deposition. We observe that DNA from aquatic plants was abundant in background sediment, while embedded detrital event layers (sediment deposited under erosion events) primarily contained terrestrial plants; hence, vertical mobility of aquatic plant DNA across sediment layers was negligible within our studied lakes. About 33% of the identified terrestrial plant genera were only found in detrital sediment, suggesting that sediment origin had a strong impact on the reconstructed plant community. Similarly, DNA of some mammalian taxa (Capra hircus, Ursus arctos, Lepus, and Felis) were only or preferentially found in detrital event layers. Temporal changes across the Holocene were the main drivers of change for reconstructed plant communities, but sediment type was the second most important factor of variance. Our results highlight that erosion and sediment provenance need to be considered when reconstructing past mammalian and plant communities using environmental DNA from lake sediments

Quaternary environmental changes in tropical Lake Towuti, Indonesia, inferred from end‐member modelling of X‐ray fluorescence core‐scanning data

Continental and marine sediments are composed of a mixture from different sources and are influenced by a variety of environmental factors and transport processes prior to deposition. For analysis and interpretation, these sources and processes are often challenging to disentangle. We show that end-member modelling of X-ray fluorescence (XRF) core-scanning data helps to overcome these challenges by unmixing different environmental signals from high-resolution sediment geochemical records. We apply this approach to a 100 m long lacustrine succession from Lake Towuti, Indonesia, to separate the regional climate and tectonic history from local ecological and diagenetic processes. The resulting six end-members (EMs) are interpreted to represent changes in ecological (EM1), climatic (EMs 2–4), tectonic (EM 5) and geomorphic (EM6) processes determining changes in sediment composition. Because end-member analysis allows for the tracking of transient and overlapping processes, climatic changes can be followed throughout the 100 m-long succession, suggesting alternating wet and dry periods in Central Sulawesi over long (several 100 000 years) time scales. We show that end-member analysis on elemental data sets offers a detailed and objective means to disentangle depositional processes in sedimentary successions resulting from varying tectonic and environmental factors involved in sediment formation and deposition

The topological nature of tag jumping in environmental DNA metabarcoding studies

Metabarcoding of environmental DNA constitutes a state-of-the-art tool for environmental studies. One fundamental principle implicit in most metabarcoding studies is that individual sample amplicons can still be identified after being pooled with others—based on their unique combinations of tags—during the so-called demultiplexing step that follows sequencing. Nevertheless, it has been recognized that tags can sometimes be changed (i.e., tag jumping), which ultimately leads to sample crosstalk. Here, using four DNA metabarcoding data sets derived from the analysis of soils and sediments, we show that tag jumping follows very specific and systematic patterns. Specifically, we find a strong correlation between the number of reads in blank samples and their topological position in the tag matrix (described by vertical and horizontal vectors). This observed spatial pattern of artefactual sequences could be explained by polymerase activity, which leads to the exchange of the 3′ tag of single stranded tagged sequences through the formation of heteroduplexes with mixed barcodes. Importantly, tag jumping substantially distorted our data sets—despite our use of methods suggested to minimize this error. We developed a topological model to estimate the noise based on the counts in our blanks, which suggested that 40%–80% of the taxa in our soil and sedimentary samples were likely false positives introduced through tag jumping. We highlight that the amount of false positive detections caused by tag jumping strongly biased our community analyses

Iron Mineralogy and Sediment Color in a 100 m Drill Core from Lake Towuti, Indonesia Reflect Catchment and Diagenetic Conditions

Iron is the most abundant redox-sensitive element on the Earth’s surface, and the oxidation state, mineral host, and crystallinity of Fe-rich phases in sedimentary systems can record details of water-rock interactions and environmental conditions. However, we lack a complete understanding of how these Fe-rich materials are created, maintained, and oxidized or reduced in sedimentary environments, particularly those with mafic sources. The catchment of Lake Towuti, Indonesia, is known to contain a wide range of abundant crystalline Fe oxide, and the lake has a long sedimentary history. Here we study a ∼100 m long drill core from the lake to understand patterns of sedimentation and how young iron-rich sediments are affected by diagenesis through geologic time. We use visible/near infrared and Mössbauer spectroscopy, X-ray diffraction, bulk chemistry measurements, and statistical cluster analysis to characterize the core sediment. We find that the core sediment can be divided into three statistically different zones dominated by Mg serpentine, Al clay minerals, and Fe2+ carbonate, respectively. The entire core is rich in nanophase Fe, and elemental correlations and Fe mineralogy vary between these zones. The nanophase Fe is highly complex with both ferrous and ferric components, and contributes to, but does not dictate, variations in sediment color. We propose that the distinctive zones are the result of structural basin changes (notably river capture and shifting drainage patterns), and diagenetic overprinting caused by deep burial of reactive Fe. This complex record has implications for disentangling depositional and diagenetic trends in other mafic lacustrine systems

Seasonality of cladoceran and bryozoan resting stage δ13C values and implications for their use as palaeolimnological indicators of lacustrine carbon cycle dynamics

The stable carbon isotope composition, expressed as δ13C values, of chitinous resting stages of planktivorous invertebrates can provide information on past changes in carbon cycling in lakes. For example, the δ13C values of cladoceran ephippia and bryozoan statoblasts have been used to estimate the past contribution of methane-derived carbon to lake food webs and variations in the δ13C value of planktonic algae. Limited information, however, is available concerning seasonal variations in δ13C values of these organisms and their resting stages. We measured the seasonal variation in δ13C values of Daphnia (Branchiopoda: Cladocera: Daphniidae) and their floating ephippia over a 2-year period in small, dimictic Lake Gerzensee, Switzerland. Floating ephippia of Ceriodaphnia (Branchiopoda: Cladocera: Daphniidae) and statoblasts of Plumatella (Phylactolaemata: Plumatellida: Plumatellidae) were analysed during parts of this period. Furthermore, δ13C values of remains from all three organism groups were analysed in a 62-cm-long sediment core. Throughout the year, Daphnia δ13C values tracked the δ13C values of particulate organic matter (POM), but were more negative than POM, indicating that Daphnia also utilize a relatively 13C-depleted carbon source. Daphnia ephippia δ13C values did not show any pronounced seasonal variation, suggesting that they are produced batch-wise in autumn and/or spring and float for several months. In contrast, δ13C values of Ceriodaphnia ephippia and Plumatella statoblasts followed variations in δ13CPOM values, Ceriodaphnia values being the most negative of the resting stages. Average cladoceran ephippia δ13C values in the flotsam agreed well with ephippia values from Gerzensee surface sediments. In contrast, average Plumatella statoblast δ13C values from the flotsam were 4‰ more negative than in the surface sediments. In the sediment core, δ13C values of the two cladocerans remained low (mean −39.0 and −41.9‰) throughout the record. In contrast, Plumatella had distinctly less negative δ13C values (mean −32.0‰). Our results indicate that in Gerzensee, Daphnia and Ceriodaphnia strongly relied on a 13C-depleted food source throughout the past 150 years, most likely methane-oxidising bacteria, whereas this food source was not a major contribution to the diet of bryozoans

Climatic and tectonic controls on source-to-sink processes in the tropical, ultramafic catchment of Lake Towuti, Indonesia

Humid tropical landscapes are subject to intense weathering and erosion, which strongly influence sediment mobilisation and deposition. In this setting, we aimed to understand how geomorphology and hydroclimate altered the style and intensity of erosion and sediment composition in a tropical lake and its tectonically active catchment. Lake Towuti (2.75 degrees S, 121.5 degrees E) is one of the oldest and deepest lakes in Indonesia, with uninterrupted lacustrine sedimentation over several glacial-interglacial cycles. Here we present results from a novel set of Lake Towuti surface sediment, bedrock and soil samples from the catchment, and two existing sediment cores that extend to 30,000 and 60,000years before present. We studied the catchment morphology, soil properties, geochemistry, and clay and bulk mineralogy. Results from several river long profiles show clear signs of tectonic activity, which enhances river incision, favours mass movement processes, and together with remobilisation of fluvial deposits, strongly influences modern sedimentation in the lake. Material from the Mahalona River, the lake's largest inflow, dominates modern sediment composition in Towuti's northern basin. The river transports Al-poor and Mg-rich sediments (mainly serpentines) to the lake, indicating river incision into the Mg-rich serpentinised peridotite bedrock. Relatively small, but important additional contributions of material, come from direct laterite-derived input and the Loeha River, which both provide Al-rich and Mg-poor sediment to the lake. Over time, the Al/Mg and kaolinite-to-serpentine ratios varied strongly, primarily in response to lake-level fluctuations driven by hydroclimatic changes. In the past 60,000years, both the Al/Mg and kaolinite-to-serpentine ratios showed variations sensitive to changes in climate boundary conditions across glacial-interglacial cycles, while tectonic activity had less influence on changes in sediment composition on these short time-scales

Geochemical analyses from different surface sediment samples of Lake Towuti, Indonesia

For granulometric, geochemical and mineralogical analyses, approximately 25 ml of each surface sample was frozen for 24 hours and subsequently lyophilized using a Christ BETA 1-8 LDplus (Martin Christ Gefriertrocknungsanlagen GmbH, Osterode am Harz, Germany). The freeze-dried samples were homogenized and split into two aliquots. The other aliquot of the freeze-dried surface samples was ground to <63 µm with a Planetary Mill Pulverisette 5 (FRITSCH GmbH, Idar-Oberstein, Germany) and used for mineralogical and geochemical analyses. For quantitative analyses of the inorganic element composition of the surface samples, including concentrations of selected major, minor and trace elements (Ti, K, Al, Mg, Ca, Fe, Cr and Mn), 0.5 g of dry and ground bulk sample material was digested using a near-total digestion protocol with HCl, nitric (HNO3), perchloric (HClO4) and hydrofluoric (HF) acids in heated and closed teflon vessels. Measurements were performed by means of inductively coupled plasma-mass spectroscopy (ICP-MS) at Activation Laboratories Ltd., Ancaster, ON, Canada. Separate Si measurements were conducted by energy-dispersive X-ray fluorescence (ED-XRF) using a portable analyzer (NITON XL3t; Thermo Fisher Scientific, Waltham, MA, USA) at the University of Cologne, Germany. Triplicate measurements were performed on pellets of freeze-dried and ground sample aliquots, which were pressed into teflon rings under 12 bars, and subsequently covered with a 4 µm polypropylene film (X-ray film, TF-240-255, Premier Lab Supply, Port St. Lucie, FL, USA). Measurements were performed using a gold anode X-ray source (70 kV) and the 'mining-minerals-mode'. The secondary X-rays of element-specific photon energies were detected with a silicon drift detector and processed by a digital signal processor. Si concentrations (in ppm) were calculated from the element-specific fluorescence energies and compared with external and internal reference materials (STDS-4, BCR142R and BCR-CRM 277)

Magnetic susceptibility measurements from different surface sediment samples of Lake Towuti, Indonesia

The mass magnetic susceptibility (MS) was analyzed on wet bulk sediment aliquots using a KLY-2 Kappabridge (AGICO, Brno, Czech Republic). MS measurements were carried out on sample containers of 2 x 2 x 1.6 cm (i.e. a sample volume of 6.4 cm3), which frequently are used for palaeo and rock magnetic measurements. The only exceptions are samples 12 and 33, which did not contain sufficient material

Grain-size distribution from different surface sediment samples of Lake Towuti, Indonesia

A digital elevation model (DEM) of Lake Towuti and its surrounding was calculated using ArcGIS (Esri, Inc., Redlands, CA, USA). The model is based on open source satellite data for Sulawesi provided by the United States Geological Survey (Aster Global DEM based on the Shuttle Radar Topography Mission carried out by the National Aeronautics and Space Administration at 1 arc-second 30 m spatial resolution). Spatial interpolation of the analytical surface sediment data was carried out with the software Surfer 9 (Golden Software Inc., Golden, CO, USA) using the kriging method. Statistical analyses employed on the surface sediment data sets comprise end-member (EM) unmixing, principal component analysis (PCA) and a redundancy analysis (RDA). EM analyses were carried out on normalized and standardized grain-size (EMGS), chemical (EMChem) and mineralogical (EMMin) data sets. Assuming a sedimentary mixture from different sources the mixing model in all cases can be written as: X = AS + E (1) where X represents the n-by-m matrix of n samples (one per row) and m variables (relative abundance of individual data). Matrix A (n-by-l) denotes the mixing proportion of l end-members for the n samples, S represents the m properties of the l EMs and E is the error matrix of residuals. The uncertainties of the EM analyses are controlled by the errors of the data sets used. The EM algorithm developed by Heslop and Dillon (2007) adopting the approach of Weltje (1997) was applied. The decision criterion of how many EMs are included in the three models is based partly on the coefficients of determination derived from the PCA. Nevertheless, the number of the respective EMs should also be reasonable in the geological context of the data set (Weltje, 1997; Weltje and Prins, 2007). Residuals of the EM models include analytical errors and non-identified additional sources of variability. All other multivariate statistical analyses were carried out with the Excel-based software Addinsoft XLSTAT (STATCON GmbH, Witzenhausen, Germany) The PCA was conducted with the sand content and the concentrations of selected elements determined by ICP-MS and XRF analyses (Fe, Mg, Al, Si, K, Ca, Cr and Ni). In the RDA, the results derived from the PCA are expanded by the concentrations of major minerals, the MS and TOC values and the C/N ratio. The correlation matrix includes all data except 13COM and the concentrations of diatom frustules, sponge spicules and tephra particles, which all were determined on a subset of the surface samples only