Transient social-ecological dynamics reveal signals of decoupling in a highly disturbed Anthropocene landscape.

Understanding the transient dynamics of interlinked social-ecological systems (SES) is imperative for assessing sustainability in the Anthropocene. However, how to identify critical transitions in real-world SES remains a formidable challenge. In this study, we present an evolutionary framework to characterize these dynamics over an extended historical timeline. Our approach leverages multidecadal rates of change in socioeconomic data, paleoenvironmental, and cutting-edge sedimentary ancient DNA records from China's Yangtze River Delta, one of the most densely populated and intensively modified landscapes on Earth. Our analysis reveals two significant social-ecological transitions characterized by contrasting interactions and feedback spanning several centuries. Initially, the regional SES exhibited a loosely connected and ecologically sustainable regime. Nevertheless, starting in the 1950s, an increasingly interconnected regime emerged, ultimately resulting in the crossing of tipping points and an unprecedented acceleration in soil erosion, water eutrophication, and ecosystem degradation. Remarkably, the second transition occurring around the 2000s, featured a notable decoupling of socioeconomic development from ecoenvironmental degradation. This decoupling phenomenon signifies a more desirable reconfiguration of the regional SES, furnishing essential insights not only for the Yangtze River Basin but also for regions worldwide grappling with similar sustainability challenges. Our extensive multidecadal empirical investigation underscores the value of coevolutionary approaches in understanding and addressing social-ecological system dynamics.

Human-triggered magnification of erosion rates in European Alps since the Bronze Age.

A major feature of the Anthropocene is the drastic increase in global soil erosion. Soil erosion is threatening Earth habitability not only as soils are an essential component of the Earth system but also because societies depend on soils. However, proper quantification of the impact of human activities on erosion over thousands of years is still lacking. This is particularly crucial in mountainous areas, where the highest erosion rates are recorded. Here we use the Lake Bourget catchment, one of the largest in the European Alps, to estimate quantitatively the impact of human activities on erosion. Based on a multi-proxy, source-to-sink approach relying on isotopic geochemistry, we discriminate the effects of climate fluctuations from those of human activities on erosion over the last 10,000 years. We demonstrate that until 3800 years ago, climate is the only driver of erosion. From that time on, climate alone cannot explain the measured rates of erosion. Thanks to an unprecedented regional paleoenvironmental reconstruction, we highlight that the development of pastoralism at high altitudes from the Bronze Age onwards and the extension of agriculture starting in the Middle Ages were key factors in the drastic increase in erosion observed in the Alps.

The legacy of metallurgical atmospheric contamination in a mountainous catchment: A delayed response of Pb contamination.

Metal-rich fumes emitted during ore smelting contribute to widespread anthropogenic contamination. Environmental archives (such as lake sediments) record fallouts deposited on lake and terrestrial surfaces during ancient mining and smelting activities. However, very few is known about the potential buffering effect of soils upon which metal falls out, prior to be released through runoff and or/erosion, hence leading to pervasive contamination fluxes long after the ceasing of metallurgical activities. Here we aim at assessing this long-term remobilisation in a mountainous catchment area. Lake sediments and soils were collected 7 km upward a 200-year-old historic mine. The PbAg mine of Peisey-Nancroix was operated between the 17th and the 19th centuries with a documented smelting period of 80 years. In lake sediments, the total Pb content varies from 29 mg.kg-1 prior smelting to 148 mg.kg-1 during ore smelting. Pb isotopes in lake sediments and soils provide evidence of anthropogenic Pb from the local ore (206Pb/207Pb = 1.173; 208Pb/206Pb = 2.094) during and after smelting, suggesting anthropogenic Pb remobilisation for 200 years. The accumulation rates of anthropogenic Pb calculated in lake sediments after the smelting period confirm such a remobilisation. Despite a decrease in this accumulation rate through time, soils still contain significant stocks of anthropogenic Pb (54-89 % of PbANTH). The distribution of present-day anthropogenic Pb in the catchment area depends mainly on topographic characteristics. Coupling lake sediments and soils investigations is thus necessary to constrain the long-term persistence and remobilisation of a diffuse contamination related to mining activities.

Sedimentary structure discrimination with hyperspectral imaging in sediment cores.

Hyperspectral imaging (HSI) is a non-destructive, high-resolution imaging technique that is currently under significant development for analyzing geological areas with remote devices or natural samples in a laboratory. In both cases, the hyperspectral image provides several sedimentary structures that must be separated to temporally and spatially describe the sample. Sediment sequences are composed of successive deposits (strata, homogenite, flood) that are visible depending on sample properties. The classical methods to identify them are time-consuming, have a low spatial resolution (millimeters) and are generally based on naked-eye counting. In this study, we compare several supervised classification algorithms to discriminate sedimentological structures in lake sediments. Instantaneous events in lake sediments are generally linked to extreme geodynamical events (e.g., floods, earthquakes), so their identification and counting are essential to understand long-term fluctuations and improve hazard assessments. Identification and counting are done by reconstructing a chronicle of event layer occurrence, including estimation of deposit thicknesses. Here, we applied two hyperspectral imaging sensors (Visible Near-Infrared, VNIR, 60 µm, 400-1000 nm; Short Wave Infrared, SWIR, 200 µm, 1000-2500 nm) on three sediment cores from different lake systems. We highlight that the SWIR sensor is the optimal one for creating robust classification models with discriminant analyses (prediction accuracies of 0.87-0.98). Indeed, the VNIR sensor is impacted by the surface reliefs and structures that are not in the learning set, which causes mis-classification. These observations are also valid for the combined sensor (VNIR-SWIR) and the RGB images. Several spatial and spectral pre-processing were also compared and enabled one to highlight discriminant information specific to a sample and a sensor. These works show that the combined use of hyperspectral imaging and machine learning improves the characterization of sedimentary structures compared to conventional methods.

Evidence of Chlordecone Resurrection by Glyphosate in French West Indies.

The widespread use of pesticides in agriculture during the last several decades has contaminated soils and different Critical Zone (CZ) compartments, defined as the area extended from the top of the vegetation canopy to the groundwater table, and it integrates interactions of the atmosphere, lithosphere, biosphere, and hydrosphere. However, the long-term fate, storage, and transfer dynamics of persistent pesticides in CZ in a changing world remain poorly understood. In the French West Indies, chlordecone (CLD), a toxic organochlorine insecticide, was extensively applied to banana fields to control banana weevil from 1972 to 1993 after which it was banned. Here, to understand CZ trajectories we apply a retrospective observation based on marine sediment core analyses to monitor long-term CLD transfer, fate, and consequences in Guadeloupe and Martinique islands. Both CLD profiles show synchronous chronologies. We hypothesized that the use of glyphosate, a postemergence herbicide, from the late 1990s onward induced CZ modification with an increase in soil erosion and led to the release of the stable CLD stored in the soils of polluted fields. CLD fluxes drastically increased when glyphosate use began, leading to widespread ecosystem contamination. As glyphosate is used globally, ecotoxicological risk management strategies should consider how its application affects persistent pesticide storage in soils, transfer dynamics, and widespread contamination.

When archives are missing, deciphering the effects of public policies and climate variability on the Brazilian semi-arid region using sediment core studies.

The northeastern region of Brazil is the most densely populated and biodiverse semi-arid regions of the planet. Effects of the natural climate variability and colonization on the landscape have been described since the beginning of the 16th century but little is known about their effects on natural resources. Climate projections predict temperatures above 40 °C and an increase in the number and duration of droughts at the end of the 21st century with strong societal impacts. Here, we analyze the influence of public policies, human activities and natural climate variability on the environment over the last 60 years. Our study is based on sedimentological and environmental reconstructions from two sediment cores collected in two dam lakes on the river Acaraú in the State of Ceará. Multiproxy analyses of both cores (inorganic geochemistry, pollen, charcoal, remote sensing) at an annual resolution showed that 1) at interannual scale composition and distribution of the dry forest (known as Caatinga) were not affected by the alternance of drought and high moisture episodes; 2) at decadal scale human activities such as agriculture were reflected by changes in vegetation cover and fishery by progressive changes in lake trophic status; 3) public policies were able to promote changes in the landscape e.g., land colonization with the regression of the dry forest and irrigation plan able to amplify the deforestation and change the floristic composition. Thanks to paleo-science approach, our environmental diagnosis should help future decision-making and provide guidelines for preservation of resources and wellbeing of the inhabitants.

High-resolution prediction of organic matter concentration with hyperspectral imaging on a sediment core.

In the case of environmental samples, the use of a chemometrics-based prediction model is highly challenging because of the difficulty in experimentally creating a well-ranged reference sample set. In this study, we present a methodology using short wave infrared hyperspectral imaging to create a partial least squares regression model on a cored sediment sample. It was applied to a sediment core of the well-known Lake Bourget (Western Alps, France) to develop and validate a model for downcore high resolution LOI550 measurements used as a proxy of the organic matter. In lake and marine sediment, the organic matter content is widely used, for example, to reconstruct carbon flux variations through time. Organic matter analysis through routine analysis methods is time- and material-consuming, as well as not spatially resolved. A new instrument based on hyperspectral imaging allows high spatial and spectral resolutions to be acquired all along a sediment core. In this study, we obtain a model characterized by a 0.95 r prediction, with 0.77 wt% of model uncertainty based on 27 relevant wavelengths. The concentration map shows the variation inside each laminae and flood deposit. LOI550 reference values obtained with the loss on ignition are highly correlated to the inc/coh ratio used as a proxy of the organic matter in X-ray fluorescence with a correlation coefficient of 0.81. This ratio is also correlated with the averaged subsampled hyperspectral prediction with a r of 0.65.

DNA from lake sediments reveals long-term ecosystem changes after a biological invasion.

What are the long-term consequences of invasive species? After invasion, how long do ecosystems require to reach a new equilibrium? Answering these questions requires long-term, high-resolution data that are vanishingly rare. We combined the analysis of environmental DNA extracted from a lake sediment core, coprophilous fungi, and sedimentological analyses to reconstruct 600 years of ecosystem dynamics on a sub-Antarctic island and to identify the impact of invasive rabbits. Plant communities remained stable from AD 1400 until the 1940s, when the DNA of invasive rabbits was detected in sediments. Rabbit detection corresponded to abrupt changes of plant communities, with a continuous decline of a dominant plant species. Furthermore, erosion rate abruptly increased with rabbit abundance. Rabbit impacts were very fast and were stronger than the effects of climate change during the 20th century. Lake sediments can allow an integrated temporal analysis of ecosystems, revealing the impact of invasive species over time and improving our understanding of underlying mechanisms.

Resurrection ecology in Artemia.

Resurrection ecology (RE) is a very powerful approach to address a wide range of question in ecology and evolution. This approach rests on using appropriate model systems, and only few are known to be available. In this study, we show that Artemia has multiple attractive features (short generation time, cyst bank and collections, well-documented phylogeography, and ecology) for a good RE model. We show in detail with a case study how cysts can be recovered from sediments to document the history and dynamics of a biological invasion. We finally discuss with precise examples the many RE possibilities with this model system: adaptation to climate change, to pollution, to parasites, to invaders and evolution of reproductive systems.

Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming.

High-throughput sequencing of sedimentary DNA (sed-DNA) was utilized to reconstruct the temporal dynamics of microbial eukaryotic communities (MECs) at a centennial scale in two re-oligotrophicated lakes that were exposed to different levels of phosphorus enrichment. The temporal changes within the MECs were expressed in terms of richness, composition and community structure to investigate their relationships with two key forcing factors (i.e., nutrient enrichment and climate warming). Various groups, including Apicomplexa, Cercozoa, Chrysophyceae, Ciliophora, Chlorophyceae and Dinophyceae, responded to phosphorus enrichment levels with either positive or negative impacts on their richness and relative abundance. For both lakes, statistical modelling demonstrated that phosphorus concentration ([P]) was a dominant contributor to MECs modifications before the 1980s; after the mid-80s, the contribution of air temperature changes increased and potentially surpassed the contribution of [P]. Co-occurrence network analysis revealed that some clusters of taxa (i.e., modules) composed mainly of Dinophyceae and unclassified Alveolata were strongly correlated to air temperature in both lakes. Overall, our data showed that sed-DNA constitutes a precious archive of information on past biodiversity changes, allowing the study of the dynamics of numerous eukaryotic groups that were not traditionally considered in paleo-reconstructions.

Long-term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA.

Assessing the extent to which changes in lacustrine biodiversity are affected by anthropogenic or climatic forces requires extensive palaeolimnological data. We used high-throughput sequencing to generate time-series data encompassing over 2200 years of microbial eukaryotes (protists and Fungi) diversity changes from the sedimentary DNA record of two lakes (Lake Bourget in French Alps and Lake Igaliku in Greenland). From 176 samples, we sequenced a large diversity of microbial eukaryotes, with a total 16 386 operational taxonomic units distributed within 50 phylogenetic groups. Thus, microbial groups, such as Chlorophyta, Dinophyceae, Haptophyceae and Ciliophora, that were not previously considered in lacustrine sediment record analyses appeared to be potential biological markers of trophic status changes. Our data suggest that shifts in relative abundance of extant species, including shifts between rare and abundant taxa, drive ecosystem responses to local and global environmental changes. Community structure shift events were concomitant with major climate variations (more particularly in Lake Igaliku). However, this study shows that the impacts of climatic fluctuations may be overpassed by the high-magnitude eutrophication impacts, as observed in the eutrophicated Lake Bourget. Overall, our data show that DNA preserved in sediment constitutes a precious archive of information on past biodiversity changes.

Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity.

Studies based on the coupling of a paleolimnological approach and molecular tools (e.g., sequencing of sedimentary DNA) present a promising opportunity to obtain long-term data on past lacustrine biodiversity. However, certain validations are still required, such as the evaluation of DNA preservation in sediments for various planktonic taxa that do not leave any morphological diagnostic features. In this study, we focused on the diversity of planktonic unicellular eukaryotes and verified the presence of their DNA in sediment archives. We compared the molecular inventories (high-throughput sequencing of 18S ribosomal DNA) obtained from monitoring the water column with those obtained for DNA archived in the first 30 cm of sediment. Seventy-one percent of taxonomic units found in the water samples were detected in sediment samples, including pigmented taxa, such as Chlorophyta, Dinophyceae, and Chrysophyceae, phagotrophic taxa, such as Ciliophora, parasitic taxa, such as Apicomplexa and Chytridiomycota, and saprotrophs, such as Cryptomycota. Parallel analysis of 18S ribosomal RNA (rRNA) transcripts revealed the presence of living eukaryotic taxa only in the top 2 cm of sediment; although some limits exist in using RNA/DNA ratio as indicator of microbial activity, these results suggested that the sedimentary DNA mostly represented DNA from past and inactive communities. Only the diversity of a few groups, such as Cryptophyta and Haptophyta, seemed to be poorly preserved in sediments. Our overall results showed that the application of sequencing techniques to sedimentary DNA could be used to reconstruct past diversity for numerous planktonic eukaryotic groups.

Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA.

Paleoenvironmental studies are essential to understand biodiversity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes. SedaDNA-based reconstructions of ancient environments often rely on indicator taxa or expert knowledge, but quantitative ecological analyses might provide more objective information. Here, we analysed sedaDNA to investigate plant community trajectories in the catchment of a high-elevation lake in the Alps over the last 6400 years. We combined data on past and present plant species assemblages along with sedimentological and geochemical records to assess the relative impact of human activities through pastoralism, and abiotic factors (temperature and soil evolution). Over the last 6400 years, we identified significant variation in plant communities, mostly related to soil evolution and pastoral activities. An abrupt vegetational change corresponding to the establishment of an agropastoral landscape was detected during the Late Holocene, approximately 4500 years ago, with the replacement of mountain forests and tall-herb communities by heathlands and grazed lands. Our results highlight the importance of anthropogenic activities in mountain areas for the long-term evolution of local plant assemblages. SedaDNA data, associated with other paleoenvironmental proxies and present plant assemblages, appear to be a relevant tool for reconstruction of plant cover history. Their integration, in conjunction with classical tools, offers interesting perspectives for a better understanding of long-term ecosystem dynamics under the influence of human-induced and environmental drivers.

Historical profiles of PCB in dated sediment cores suggest recent lake contamination through the "halo effect".

We investigated the major sources of polychlorinated biphenyls (PCB) and interpreted the environmental fate processes of these persistent organic pollutants in the past and current PCB contamination of three large, urbanized, French peri-alpine lakes. Dated sediment cores were analyzed in order to reconstruct and compare the historical contamination in all three lakes. Stratigraphic changes of PCB contents and fluxes were considered as revealing the temporal dynamics of PCB deposition to the lakes and the distribution of the seven indicator congeners (further referred to as PCBi) as an indicator of the main contamination origin and pathway. Although located within a single PCB industrial production region, concentration profiles for the three lakes differed in timing, peak concentration magnitudes, and in the PCBi congeners compositions. PCBi fluxes to the sediment and the magnitude of the temporal changes were generally much lower in Lake Annecy (0.05-2 ng·cm(-2)·yr(-1)) as compared to Lakes Geneva (0.05-5 ng·cm(-2)·yr(-1)) and Bourget (5-290 ng·cm(-2)·yr(-1)). For all three lakes, the paramount contamination occurred in the early 1970s. In Lakes Annecy and Bourget, PCB fluxes have declined and plateaued at 0.5 and 8 ng·cm(-2)·yr(-1), respectively, since the early 1990s. In Lake Geneva, PCB fluxes have further decreased by the end of the XX(th) century and are now very low. For the most contaminated lake (Lake Bourget), the high PCBi flux (5-290 ng·cm(-2)·yr(-1)) and the predominance of heavy congeners for most of the time period are consistent with a huge local input to the lake. This still high rate of Lake Bourget is explained by transport of suspended solids from one of its affluents, polluted by an industrial point source. Intermediate historical levels and PCBi distribution over time for Lake Geneva suggest a mixed contamination (urban point sources and distant atmospheric transport), while atmospheric deposition to Lake Annecy explains its lowest contamination rate. The presently low contamination levels recorded in Lake Geneva correspond to atmospheric inputs, but the recent PCBi distribution of Lake Annecy, enriched in relatively heavy congeners, reveals a contamination by the neighboring Lake Bourget, following a halo effect of about 40 km radius.

Long-term relationships among pesticide applications, mobility, and soil erosion in a vineyard watershed.

Agricultural pesticide use has increased worldwide during the last several decades, but the long-term fate, storage, and transfer dynamics of pesticides in a changing environment are poorly understood. Many pesticides have been progressively banned, but in numerous cases, these molecules are stable and may persist in soils, sediments, and ice. Many studies have addressed the question of their possible remobilization as a result of global change. In this article, we present a retro-observation approach based on lake sediment records to monitor micropollutants and to evaluate the long-term succession and diffuse transfer of herbicides, fungicides, and insecticide treatments in a vineyard catchment in France. The sediment allows for a reliable reconstruction of past pesticide use through time, validated by the historical introduction, use, and banning of these organic and inorganic pesticides in local vineyards. Our results also revealed how changes in these practices affect storage conditions and, consequently, the pesticides' transfer dynamics. For example, the use of postemergence herbicides (glyphosate), which induce an increase in soil erosion, led to a release of a banned remnant pesticide (dichlorodiphenyltrichloroethane, DDT), which had been previously stored in vineyard soil, back into the environment. Management strategies of ecotoxicological risk would be well served by recognition of the diversity of compounds stored in various environmental sinks, such as agriculture soil, and their capability to become sources when environmental conditions change.

Long livestock farming history and human landscape shaping revealed by lake sediment DNA.

The reconstruction of human-driven, Earth-shaping dynamics is important for understanding past human/environment interactions and for helping human societies that currently face global changes. However, it is often challenging to distinguish the effects of the climate from human activities on environmental changes. Here we evaluate an approach based on DNA metabarcoding used on lake sediments to provide the first high-resolution reconstruction of plant cover and livestock farming history since the Neolithic Period. By comparing these data with a previous reconstruction of erosive event frequency, we show that the most intense erosion period was caused by deforestation and overgrazing by sheep and cowherds during the Late Iron Age and Roman Period. Tracking plants and domestic mammals using lake sediment DNA (lake sedDNA) is a new, promising method for tracing past human practices, and it provides a new outlook of the effects of anthropogenic factors on landscape-scale changes.

Local forcings affect lake zooplankton vulnerability and response to climate warming.

While considerable insights on the ecological consequences of climate change have been gained from studies conducted on remote lakes, little has been done on lakes under direct human exposure. Ecosystem vulnerability and responses to climate warming might yet largely depend on the ecological state and thus on local anthropogenic pressures. We tested this hypothesis through a paleolimnological approach on three temperate large lakes submitted to rather similar climate warming but varying intensities of analogous local forcings (changes in nutrient inputs and fisheries management practices). Changes in the structure of the cladoceran community were considered as revealing for alterations, over the time, of the pelagic food web. Trajectories of the cladoceran communities were compared among the three study lakes (Lakes Geneva, Bourget, and Annecy) over the last 70-150 years. Generalized additive models were used to develop a hierarchical understanding of the respective roles of local stressors and climate warming in structuring cladoceran communities. The cladoceran communities were not equally affected by climate warming between lakes. In Lake Annecy, which is the most nutrient-limited, the cladoceran community was essentially controlled by local stressors, with very limited impact of climate. In contrast, the more nutrient-loaded Lakes Geneva and Bourget were more sensitive to climate warming, although the magnitude of their responses and the pathways under which climate warming affected the communities varied between the two lakes. Finally, our results demonstrated that lake vulnerability and responses to climate warming are modulated by lake trophic status but can also be altered by fisheries management practices through changes in fish predation pressure.

Quantitative PCR enumeration of total/toxic Planktothrix rubescens and total cyanobacteria in preserved DNA isolated from lake sediments.

The variability of spatial distribution and the determinism of cyanobacterial blooms, as well as their impact at the lake scale, are still not understood, partly due to the lack of long-term climatic and environmental monitoring data. The paucity of these data can be alleviated by the use of proxy data from high-resolution sampling of sediments. Coupling paleolimnological and molecular tools and using biomarkers such as preserved DNA are promising approaches, although they have not been performed often enough so far. In our study, a quantitative PCR (qPCR) technique was applied to enumerate total cyanobacterial and total and toxic Planktothrix communities in preserved DNA derived from sediments of three lakes located in the French Alps (Lake Geneva, Lake Bourget, and Lake Annecy), containing a wide range of cyanobacterial species. Preserved DNA from lake sediments was analyzed to assess its quality, quantity, and integrity, with further application for qPCR. We applied the qPCR assay to enumerate the total cyanobacterial community, and multiplex qPCR assays were applied to quantify total and microcystin-producing Planktothrix populations in a single reaction tube. These methods were optimized, calibrated, and applied to sediment samples, and the specificity and reproducibility of qPCR enumeration were tested. Accurate estimation of potential inhibition within sediment samples was performed to assess the sensitivity of such enumeration by qPCR. Some precautions needed for interpreting qPCR results in the context of paleolimnological approaches are discussed. We concluded that the qPCR assay can be used successfully for the analysis of lake sediments when DNA is well preserved in order to assess the presence and dominance of cyanobacterial and Planktothrix communities.